From e10eb96bed3fd147f0716454c5aa7accac53b63f Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Tue, 3 Dec 2024 17:58:32 +0800 Subject: [PATCH 1/7] add wrf 3.8.1 --- package/bisheng/4.1.0/install.sh | 11 ++ package/pnetcdf/1.9.0/install.sh | 13 ++ proxy.sh | 5 +- .../vasp/5.4.4/data.vasp.arm_clang.cpu.config | 4 + templates/wrf/3.8.1/wrf.3.8.1.config | 119 ++++++++++++++++++ 5 files changed, 150 insertions(+), 2 deletions(-) create mode 100644 package/bisheng/4.1.0/install.sh create mode 100644 package/pnetcdf/1.9.0/install.sh create mode 100644 templates/wrf/3.8.1/wrf.3.8.1.config diff --git a/package/bisheng/4.1.0/install.sh b/package/bisheng/4.1.0/install.sh new file mode 100644 index 0000000..ea7f4e6 --- /dev/null +++ b/package/bisheng/4.1.0/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -e +export bisheng_ver='BiShengCompiler-4.1.0' +arch='x86' +if [ x$(arch) = xaarch64 ];then + arch='aarch64' +fi +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/${bisheng_ver}-${arch}-linux.tar.gz +cd ${JARVIS_TMP} +. $CHECK_ROOT && yum -y install libatomic libstdc++ libstdc++-devel +tar xzvf ${JARVIS_DOWNLOAD}/${bisheng_ver}-${arch}-linux.tar.gz -C $1 --strip-components=1 diff --git a/package/pnetcdf/1.9.0/install.sh b/package/pnetcdf/1.9.0/install.sh new file mode 100644 index 0000000..5cf7701 --- /dev/null +++ b/package/pnetcdf/1.9.0/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +set -x +set -e +pnetcdf_ver='1.9.0' +. ${DOWNLOAD_TOOL} -u https://parallel-netcdf.github.io/Release/parallel-netcdf-1.9.0.tar.gz +cd ${JARVIS_TMP} +rm -rf pnetcdf-${pnetcdf_ver} +tar zxvf ${JARVIS_DOWNLOAD}/pnetcdf-${pnetcdf_ver}.tar.gz +cd pnetcdf-${pnetcdf_ver} +./configure --prefix=$1 --enable-shared --enable-fortran --enable-large-file-test +make -j16 +make install diff --git a/proxy.sh b/proxy.sh index b44a75e..6e4cb8e 100644 --- a/proxy.sh +++ b/proxy.sh @@ -17,8 +17,8 @@ echo '3) 美国高速源2' echo '4) 美国高速源3' echo '5) 韩国高速源1' echo '6) 韩国高速源2' -echo '7) Gitee高速源' -echo '8) 恢复官方源' +echo 'a) Gitee高速源' +echo 'b) 恢复官方源' read -p '你输入的数字为: ' aNum @@ -28,6 +28,7 @@ if [[ $aNum =~ ^[1-6]$ ]]; then source ./init.sh elif [[ $aNum -eq 'a' ]]; then # 备份并替换dataService.py文件 + echo "you are using the gitee source" rm -rf src/dataService.py cp src/dataService.py.fast src/dataService.py elif [[ $aNum -eq 'b' ]]; then diff --git a/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config b/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config index 4c1721b..cf6cd86 100644 --- a/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config +++ b/templates/vasp/5.4.4/data.vasp.arm_clang.cpu.config @@ -1,6 +1,10 @@ [SERVER] 11.11.11.11 +[DOWNLOAD] +vtstcode/179 http://theory.cm.utexas.edu/code/vtstcode-179.tgz + + [DEPENDENCY] # add gcc/mpi module use ${JARVIS_ROOT}/software/modulefiles diff --git a/templates/wrf/3.8.1/wrf.3.8.1.config b/templates/wrf/3.8.1/wrf.3.8.1.config new file mode 100644 index 0000000..11fbade --- /dev/null +++ b/templates/wrf/3.8.1/wrf.3.8.1.config @@ -0,0 +1,119 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +wrf/3.8.1 https://codeload.github.com/wrf-model/WRF/tar.gz/refs/tags/V3.8.1 wrf-3.8.1.tar.gz + + + +[DEPENDENCY] + +module purge +module use ./software/modulefiles +./jarvis -install kgcc/9.3.1 com +module load kgcc/9.3.1 +export CC=gcc CXX=g++ FC=gfortran + +./jarvis -install hmpi/1.1.1 gcc +module load hmpi/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort +module load hdf5/1.10.1 +./jarvis -install hdf5/1.10.1 gcc +./jarvis -install package/pnetcdf/1.9.0 gcc +module load pnetcdf/1.9.0 +./jarvis -install package/netcdf/4.4.1 gcc +./jarvis -install optimized-routines/20.02 gcc +cd ${JARVIS_TMP} + +tar -zxvf $JARVIS_DOWNLOAD/wrf-3.8.1.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/9.3.1 +module load hmpi/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort +module load pnetcdf/1.9.0 +module load netcdf/4.4.1 +module load optimized-routines/20.02 + + +[APP] +app_name = WRF +build_dir = ${WRF_DIR} +binary_dir = +case_dir = ${JARVIS_ROOT}/workloads/test_wrf + +[BUILD] +cd ${JARVIS_TMP} +cd WRF-3.8.1 + +export HDF5=`which h5diff` +export HDF5=${HDF5%/*/*} +export NETCDF=`nc-config --prefix` +export PNETCDF=`pnetcdf-config --prefix` + +export CPPFLAGS="-I$HDF5/include -I$PNETCDF/include -I$NETCDF/include" +export LDFLAGS="-L$HDF5/lib -L$PNETCDF/lib -L$NETCDF/lib -lnetcdf -lnetcdff -lpnetcdf -lhdf5_hl -lhdf5 -lz" +export WRFIO_NCD_LARGE_FILE_SUPPORT=1 + +sed -i $((`sed -n '$=' arch/configure.defaults`-2)),$((`sed -n '$=' arch/configure.defaults`))d arch/configure.defaults + +mathlib_path=$JARVIS_ROOT/software/compiler/kgcc/9.3.1/lib64/libhpc +cat >> arch/configure.defaults <&1 | tee -a compile.log + + +[CLEAN] +./clean + +[RUN] +run = dsub -s run.sh +binary = +nodes = 1 + -- Gitee From 957f419d3a1a78d6bc61534270477062a776dc59 Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Tue, 3 Dec 2024 19:16:34 +0800 Subject: [PATCH 2/7] update proxy --- package/hmpi/1.1.1/install.sh | 8 ++++++++ proxy.sh | 2 ++ 2 files changed, 10 insertions(+) diff --git a/package/hmpi/1.1.1/install.sh b/package/hmpi/1.1.1/install.sh index 0de3315..3d1b40a 100755 --- a/package/hmpi/1.1.1/install.sh +++ b/package/hmpi/1.1.1/install.sh @@ -1,9 +1,17 @@ #!/bin/bash set -x set -e + +if [[ $UseGitee -eq 1 ]]; then +. ${DOWNLOAD_TOOL} -u https://gitee.com/kp-hpc-mod/hpc-src/raw/master/hucx-1.1.1-huawei.zip -f hucx-1.1.1-huawei.zip +. ${DOWNLOAD_TOOL} -u https://gitee.com/kp-hpc-mod/hpc-src/raw/master/xucg-1.1.1-huawei.zip -f xucg-1.1.1-huawei.zip +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -f hmpi-1.1.1-huawei.zip +else . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip -f hucx-1.1.1-huawei.zip . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip -f xucg-1.1.1-huawei.zip . ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip -f hmpi-1.1.1-huawei.zip +fi + cd ${JARVIS_TMP} . $CHECK_ROOT && yum install -y perl-Data-Dumper autoconf automake libtool binutils flex rm -rf hmpi-1.1.1-huawei hucx-1.1.1-huawei xucg-1.1.1-huawei diff --git a/proxy.sh b/proxy.sh index 6e4cb8e..a1d3ff0 100644 --- a/proxy.sh +++ b/proxy.sh @@ -31,10 +31,12 @@ elif [[ $aNum -eq 'a' ]]; then echo "you are using the gitee source" rm -rf src/dataService.py cp src/dataService.py.fast src/dataService.py + export UseGitee=1 elif [[ $aNum -eq 'b' ]]; then # 恢复dataService.py文件 rm -rf src/dataService.py cp src/dataService.py.ori src/dataService.py + export UseGitee=0 else echo '无效输入，请输入 1 到 7 之间的数字' fi \ No newline at end of file -- Gitee From 0b6bebadaa28a3f0b9b210517879f309140f7adc Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Wed, 4 Dec 2024 14:32:12 +0800 Subject: [PATCH 3/7] add package --- package/darshan/1.1.0/install.sh | 25 +++++++++ package/darshan/2.3.0/install.sh | 25 +++++++++ package/darshan/3.4.6/install.sh | 25 +++++++++ package/eig/8.0.0/install.sh | 19 +++++++ package/gdal/3.7.0/install.sh | 12 +++++ package/gsl/2.7.1/install.sh | 11 ++++ package/kp-hpc/2.1.0/install.sh | 9 ++++ package/openblas/0.3.23/install.sh | 11 ++++ package/pnetcdf/1.9.0/install.sh | 4 +- package/samtools/0.1.9/install.sh | 8 +++ package/samtools/1.15/install.sh | 8 ++- templates/gsea/4.3.2/data.gsea.arm.cpu.config | 51 ++++++++++++++++++ .../0.3.23/data.openblas.arm.cpu.config | 53 +++++++++++++++++++ .../wrf.4.6.1.config} | 44 +++++++-------- 14 files changed, 277 insertions(+), 28 deletions(-) create mode 100644 package/darshan/1.1.0/install.sh create mode 100644 package/darshan/2.3.0/install.sh create mode 100644 package/darshan/3.4.6/install.sh create mode 100644 package/eig/8.0.0/install.sh create mode 100644 package/gdal/3.7.0/install.sh create mode 100644 package/gsl/2.7.1/install.sh create mode 100644 package/kp-hpc/2.1.0/install.sh create mode 100644 package/openblas/0.3.23/install.sh create mode 100644 package/samtools/0.1.9/install.sh create mode 100644 templates/gsea/4.3.2/data.gsea.arm.cpu.config create mode 100644 templates/openblas/0.3.23/data.openblas.arm.cpu.config rename templates/wrf/{3.8.1/wrf.3.8.1.config => 4.6.1/wrf.4.6.1.config} (69%) diff --git a/package/darshan/1.1.0/install.sh b/package/darshan/1.1.0/install.sh new file mode 100644 index 0000000..1d06261 --- /dev/null +++ b/package/darshan/1.1.0/install.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# please build with gcc/icc+openmpi +# gcc: export CC=mpicc +# icc: export CC=mpiicc +set -x +set -e +version='1.1.0' +. $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser zlib-devel ghostscript +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz +cd darshan-${version} +./prepare.sh +# install darshan runtime to collect IO info. +cd darshan-runtime +mkdir -p $1/runtime +./configure --prefix=$1/runtime --with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_DIR_PATH --with-jobid-env=NONE +make -j +make install +# install darshan util to analysis IO info. +cd ../darshan-util +mkdir -p $1/util +./configure --prefix=$1/util +make -j +make install \ No newline at end of file diff --git a/package/darshan/2.3.0/install.sh b/package/darshan/2.3.0/install.sh new file mode 100644 index 0000000..1c0cc1a --- /dev/null +++ b/package/darshan/2.3.0/install.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# please build with gcc/icc+openmpi +# gcc: export CC=mpicc +# icc: export CC=mpiicc +set -x +set -e +version='2.3.0' +. $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser zlib-devel ghostscript +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz +cd darshan-${version} +./prepare.sh +# install darshan runtime to collect IO info. +cd darshan-runtime +mkdir -p $1/runtime +./configure --prefix=$1/runtime --with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_DIR_PATH --with-jobid-env=NONE +make -j +make install +# install darshan util to analysis IO info. +cd ../darshan-util +mkdir -p $1/util +./configure --prefix=$1/util +make -j +make install \ No newline at end of file diff --git a/package/darshan/3.4.6/install.sh b/package/darshan/3.4.6/install.sh new file mode 100644 index 0000000..0be079b --- /dev/null +++ b/package/darshan/3.4.6/install.sh @@ -0,0 +1,25 @@ +#!/bin/bash +# please build with gcc/icc+openmpi +# gcc: export CC=mpicc +# icc: export CC=mpiicc +set -x +set -e +version='3.4.6' +. $CHECK_ROOT && yum install -y texlive* gnuplot perl-Pod-LaTeX perl-HTML-Parser zlib-devel ghostscript +. ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/darshan/releases/darshan-${version}.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/darshan-${version}.tar.gz +cd darshan-${version} +./prepare.sh +# install darshan runtime to collect IO info. +cd darshan-runtime +mkdir -p $1/runtime +./configure --prefix=$1/runtime --with-mem-align=8 --with-log-path-by-env=DARSHAN_LOG_DIR_PATH --with-jobid-env=NONE +make -j +make install +# install darshan util to analysis IO info. +cd ../darshan-util +mkdir -p $1/util +./configure --prefix=$1/util +make -j +make install \ No newline at end of file diff --git a/package/eig/8.0.0/install.sh b/package/eig/8.0.0/install.sh new file mode 100644 index 0000000..a16317c --- /dev/null +++ b/package/eig/8.0.0/install.sh @@ -0,0 +1,19 @@ +#!/bin/bash +set -x +set -e + +./jarvis -install openblas/0.3.23 clang +./jarvis -install gsl/2.7.1 clang + +wget https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz -O ${JARVIS_DOWNLOAD}/EIG-8.0.0.tar.gz + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/EIG-8.0.0.tar.gz > /dev/null 2>&1 +cd cd EIG-8.0.0/src +sed -i "1s%^.*$%override CFLAGS += -I../include -I$targetdir/openblas/openblas_install/include%g" Makefile +sed -i '10d' Makefile +sed -i '12d' Makefile +sed -i "10s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile +sed -i "11s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install diff --git a/package/gdal/3.7.0/install.sh b/package/gdal/3.7.0/install.sh new file mode 100644 index 0000000..d6eaabd --- /dev/null +++ b/package/gdal/3.7.0/install.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://download.osgeo.org/gdal/3.7.0/gdal-3.7.0.tar.xz +cd ${JARVIS_TMP} +rm -rf gdal-2.2.4 +tar -xvf ${JARVIS_DOWNLOAD}/gdal-3.7.0.tar.xz > /dev/null 2>&1 +cd gdal-3.7.0/ +mkdir build +cd build +cmake ../ +make install diff --git a/package/gsl/2.7.1/install.sh b/package/gsl/2.7.1/install.sh new file mode 100644 index 0000000..a651de9 --- /dev/null +++ b/package/gsl/2.7.1/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://ftpmirror.gnu.org/gsl/gsl-2.7.1.tar.gz +cd ${JARVIS_TMP} +rm -rf gsl-2.7.1 +tar -xvf ${JARVIS_DOWNLOAD}/gsl-2.7.1.tar.gz +cd gsl-2.7.1 +./configure --prefix=$1 +make -j +make install diff --git a/package/kp-hpc/2.1.0/install.sh b/package/kp-hpc/2.1.0/install.sh new file mode 100644 index 0000000..14067a8 --- /dev/null +++ b/package/kp-hpc/2.1.0/install.sh @@ -0,0 +1,9 @@ +#!/bin/bash +set -x +set -e +file_name=kunpeng-hpc-2.1.0-aarch64-linux +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/Kunpeng_SDK/HPC/${file_name}.tar.gz +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/${file_name}.tar.gz +cd ${file_name}/script +./install.sh \ No newline at end of file diff --git a/package/openblas/0.3.23/install.sh b/package/openblas/0.3.23/install.sh new file mode 100644 index 0000000..8b10dfa --- /dev/null +++ b/package/openblas/0.3.23/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +ver="0.3.23" +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/xianyi/OpenBLAS/archive/refs/tags/v${ver}.tar.gz -f OpenBLAS-${ver}.tar.gz +cd ${JARVIS_TMP} +rm -rf OpenBLAS-${ver} +tar -xzvf ${JARVIS_DOWNLOAD}/OpenBLAS-${ver}.tar.gz +cd OpenBLAS-${ver} +make -j 16 +make PREFIX=$1 install diff --git a/package/pnetcdf/1.9.0/install.sh b/package/pnetcdf/1.9.0/install.sh index 5cf7701..2d0a66c 100644 --- a/package/pnetcdf/1.9.0/install.sh +++ b/package/pnetcdf/1.9.0/install.sh @@ -6,8 +6,8 @@ pnetcdf_ver='1.9.0' . ${DOWNLOAD_TOOL} -u https://parallel-netcdf.github.io/Release/parallel-netcdf-1.9.0.tar.gz cd ${JARVIS_TMP} rm -rf pnetcdf-${pnetcdf_ver} -tar zxvf ${JARVIS_DOWNLOAD}/pnetcdf-${pnetcdf_ver}.tar.gz -cd pnetcdf-${pnetcdf_ver} +tar zxvf ${JARVIS_DOWNLOAD}/parallel-netcdf-1.9.0.tar.gz +cd parallel-netcdf-1.9.0 ./configure --prefix=$1 --enable-shared --enable-fortran --enable-large-file-test make -j16 make install diff --git a/package/samtools/0.1.9/install.sh b/package/samtools/0.1.9/install.sh new file mode 100644 index 0000000..ba41ff1 --- /dev/null +++ b/package/samtools/0.1.9/install.sh @@ -0,0 +1,8 @@ +#!/bin/bash +set -x +set -e +wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O ${JARVIS_DOWNLOAD}/samtools-0.1.9.tar.gz +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/samtools-0.1.9.tar.gz > /dev/null 2>&1 +cd samtools-0.1.9 +make diff --git a/package/samtools/1.15/install.sh b/package/samtools/1.15/install.sh index 357b1cb..cbfaae6 100755 --- a/package/samtools/1.15/install.sh +++ b/package/samtools/1.15/install.sh @@ -1,10 +1,8 @@ #!/bin/bash set -x set -e -. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 +wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O ${JARVIS_TMP}/samtools-0.1.9.tar.gz cd ${JARVIS_TMP} -tar xvf ${JARVIS_DOWNLOAD}/samtools-1.15.tar.bz2 -cd samtools-1.15 -./configure --prefix=$1 +tar xvf ${JARVIS_DOWNLOAD}/samtools-0.1.9.tar.gz +cd samtools-0.1.9 make -j -make install diff --git a/templates/gsea/4.3.2/data.gsea.arm.cpu.config b/templates/gsea/4.3.2/data.gsea.arm.cpu.config new file mode 100644 index 0000000..4034bff --- /dev/null +++ b/templates/gsea/4.3.2/data.gsea.arm.cpu.config @@ -0,0 +1,51 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +GSEA/4.3.2 https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip GSEA_4.3.2.zip + +[DOWNLOADORI] +GSEA/4.3.2 https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip GSEA_4.3.2.zip + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install kgcc/9.3.1 com +module load kgcc/9.3.1 + + + +[ENV] +module use ./software/modulefiles +module purge +module load kgcc/9.3.1 + +[APP] +app_name = STAR +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + + + +[BUILD] +set -x +set -e +module use ./software/modulefiles +module purge +module load kgcc/9.3.1 + + +cd ${JARVIS_TMP} +rm -rf GSEA_4.3.2 +uinzip $JARVIS_DOWNLOAD/GSEA_4.3.2.zip +cd ${JARVIS_TMP}/GSEA_4.3.2 + + +[CLEAN] +./clean_build + +[RUN] +run = +binary = +nodes = 1 diff --git a/templates/openblas/0.3.23/data.openblas.arm.cpu.config b/templates/openblas/0.3.23/data.openblas.arm.cpu.config new file mode 100644 index 0000000..943d849 --- /dev/null +++ b/templates/openblas/0.3.23/data.openblas.arm.cpu.config @@ -0,0 +1,53 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +OpenBLAS/0.3.23 $JARVIS_PROXY/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz OpenBLAS-0.3.23.tar.gz + +[DOWNLOADORI] +OpenBLAS/0.3.23 $JARVIS_PROXY/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz OpenBLAS-0.3.23.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install kgcc/9.3.1 com +module load kgcc/9.3.1 + + + +[ENV] +module use ./software/modulefiles +module purge +module load kgcc/9.3.1 + +[APP] +app_name = STAR +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + + + +[BUILD] +set -x +set -e +module use ./software/modulefiles +module purge +module load kgcc/9.3.1 + + +cd ${JARVIS_TMP} +rm -rf OpenBLAS-0.3.23 +tar -xvf $JARVIS_DOWNLOAD/OpenBLAS-0.3.23.tar.gz +cd OpenBLAS-0.3.23 +make -j 16 ARCH=aarch64 all +make PREFIX=$targetdir/openblas/openblas_install install + + +[CLEAN] +./clean_build + +[RUN] +run = +binary = +nodes = 1 diff --git a/templates/wrf/3.8.1/wrf.3.8.1.config b/templates/wrf/4.6.1/wrf.4.6.1.config similarity index 69% rename from templates/wrf/3.8.1/wrf.3.8.1.config rename to templates/wrf/4.6.1/wrf.4.6.1.config index 11fbade..6c66af1 100644 --- a/templates/wrf/3.8.1/wrf.3.8.1.config +++ b/templates/wrf/4.6.1/wrf.4.6.1.config @@ -2,8 +2,7 @@ 11.11.11.11 [DOWNLOAD] -wrf/3.8.1 https://codeload.github.com/wrf-model/WRF/tar.gz/refs/tags/V3.8.1 wrf-3.8.1.tar.gz - +wrf/4.6.1 https://codeload.github.com/wrf-model/WRF/tar.gz/refs/tags/v4.6.1 wrf-4.6.1.tar.gz [DEPENDENCY] @@ -19,13 +18,13 @@ module load hmpi/1.1.1 export CC=mpicc CXX=mpicxx FC=mpifort module load hdf5/1.10.1 ./jarvis -install hdf5/1.10.1 gcc -./jarvis -install package/pnetcdf/1.9.0 gcc -module load pnetcdf/1.9.0 -./jarvis -install package/netcdf/4.4.1 gcc +./jarvis -install package/pnetcdf/1.11.2 gcc +module load pnetcdf/1.11.2 +./jarvis -install package/netcdf/4.7.0 gcc ./jarvis -install optimized-routines/20.02 gcc cd ${JARVIS_TMP} -tar -zxvf $JARVIS_DOWNLOAD/wrf-3.8.1.tar.gz +tar -zxvf $JARVIS_DOWNLOAD/wrf-4.6.1.tar.gz [ENV] module purge @@ -33,8 +32,8 @@ module use ./software/modulefiles module load kgcc/9.3.1 module load hmpi/1.1.1 export CC=mpicc CXX=mpicxx FC=mpifort -module load pnetcdf/1.9.0 -module load netcdf/4.4.1 +module load pnetcdf/1.11.2 +module load netcdf/4.7.0 module load optimized-routines/20.02 @@ -46,7 +45,7 @@ case_dir = ${JARVIS_ROOT}/workloads/test_wrf [BUILD] cd ${JARVIS_TMP} -cd WRF-3.8.1 +cd WRF-4.6.1 export HDF5=`which h5diff` export HDF5=${HDF5%/*/*} @@ -63,7 +62,7 @@ mathlib_path=$JARVIS_ROOT/software/compiler/kgcc/9.3.1/lib64/libhpc cat >> arch/configure.defaults < Date: Wed, 4 Dec 2024 17:18:22 +0800 Subject: [PATCH 4/7] add life science --- package/deeptool/3.5.1/install.sh | 14 + package/lifescience/install.sh | 589 ++++++++++++++++++++++++++++++ package/ncbi-vdb/3.0.0/install.sh | 15 + proxy.sh | 2 +- 4 files changed, 619 insertions(+), 1 deletion(-) create mode 100644 package/deeptool/3.5.1/install.sh create mode 100644 package/lifescience/install.sh create mode 100644 package/ncbi-vdb/3.0.0/install.sh diff --git a/package/deeptool/3.5.1/install.sh b/package/deeptool/3.5.1/install.sh new file mode 100644 index 0000000..70709ca --- /dev/null +++ b/package/deeptool/3.5.1/install.sh @@ -0,0 +1,14 @@ +#!/bin/bash +set -x +set -e + + +wget https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz -O ${JARVIS_DOWNLOAD}/deepTools-3.5.1.tar.gz +yum -y install doxygen cmake +yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/deepTools-3.5.1.tar.gz + +cd deepTools-3.5.1 +python3 setup.py install diff --git a/package/lifescience/install.sh b/package/lifescience/install.sh new file mode 100644 index 0000000..f22ecb4 --- /dev/null +++ b/package/lifescience/install.sh @@ -0,0 +1,589 @@ +#!/bin/bash + +#ѧ װʹܽűҪװrandfoldִ +# sh hpc_life_science.sh randfold +#ʹӦִ +#sh hpc_life_science.sh + +#--------------------------------# +OPT=$1; + +##ȫֱ +#--------------------------------# +passwd=123456; +install_path=/home/hpc_software/ +targetdir=$install_path/BIN +source_file=$install_path/source.sh +cpu_num=`grep -c "processor" /proc/cpuinfo`; #CPU +netcard=`cat /proc/net/dev|sort -rn -k2|awk '{print $1}'|awk NR==1|awk -F ':' '{print $1}'`;# +ip_addr=`ip a|grep $netcard|grep inet|awk '{print $2}'|awk -F '/' '{print $1}'` #ipַ +osType=`cat /etc/os-release|grep ID |awk NR==1|awk -F \" '{print $2}'` +basearch=`arch` + + + +#--------------------------------# +mkdir -p $targetdir +echo install_path=$install_path >> $source_file +touch $source_file + + +#--------------------------------# +#ȫ +cd $install_path +yum -y install make gcc g++ git +yum install -y java-1.8.0-openjdk-devel.aarch64 ncurses-devel.aarch64 bzip2-devel.aarch64 python3-devel python bazel +pip3 install tensorflow + +#GSEA +function install_GSEA() { +#װjava +yum install java-11-openjdk-devel.aarch64 -y +#װӻ +#yum install xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -y +#sed -i "s/X11Forwarding no/X11Forwarding yes/g" /etc/ssh/sshd_config +#systemctl restart sshd.service +cd $install_path +wget https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip +unzip GSEA_4.3.2.zip +echo export PATH=$install_path/GSEA_4.3.2:\$PATH >> $source_file +} + +#pangolin +function install_pangolin() { +#װ +yum install python3-devel python3 python3-pip git make -y +cd $install_path +wget https://github.com/cov-lineages/pangolin/archive/refs/tags/v4.3.1.tar.gz -O pangolin-v4.3.1.tar.gz +tar xf pangolin-v4.3.1.tar.gz +cd pangolin-4.3.1 +pip3 install . -i https://pypi.tuna.tsinghua.edu.cn/simple +pip3 install git+https://github.com/cov-lineages/pangolin-data.git +pip3 install git+https://github.com/cov-lineages/scorpio.git +pip3 install git+https://github.com/cov-lineages/constellations.git +pip3 install snakemake -i https://pypi.tuna.tsinghua.edu.cn/simple +} + + + +#randfold +function install_randfold() { +cd $install_path +git clone https://github.com/eb00/randfold.git +cd randfold/src/squid-1.9g +./configure && make +cd ../ +make +echo export PATH=$install_path/randfold/src >> $source_file +} + +#blat +function install_BLAT() { +cd $install_path +wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1 -O blat-35.1.tar.gz +yum -y install libpng-devel +tar zxvf blat-35.1.tar.gz +cd blat-35.1/ +sed -i 's/jmp_buf htmlRecover/\/\/jmp_buf htmlRecover/g' src/inc/htmshell.h +export MACHTYPE=aarch64 +make +echo export PATH=$install_path/blat-35.1/bin:\$PATH >> $source_file +} + + +#BWA +function install_BWA() { +cd $install_path +wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 +tar -xvf bwa-0.7.17.tar.bz2 +cd bwa-0.7.17 && wget https://raw.githubusercontent.com/jratcliff63367/sse2neon/master/SSE2NEON.h +sed -i 's/#include /#include "SSE2NEON.h"/g' ksw.c +sed -i 's/const uint8_t rle_auxtab/\/\/const uint8_t rle_auxtab/g' rle.h |grep rle_auxtab +make +echo export PATH=$install_path/bwa-0.7.17:\$PATH >> $source_file +} + +#samtools +function install_samtools() { +#gcc-10.3.1 +cd $install_path +wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O samtools-0.1.9.tar.gz +tar -xvf samtools-0.1.9.tar.gz +cd samtools-0.1.9 +make +echo export PATH=$install_path/samtools-0.1.9:\$PATH >> $source_file +} + + +#gatk +function install_gatk() { +#blat,bwa +#blat +install_BLAT +#BWA +install_BWA +#samtools +install_samtools +cd $install_path +wget https://github.com/broadinstitute/gatk/releases/download/4.0.0.0/gatk-4.0.0.0.zip -O gatk-4.0.0.0.zip +unzip gatk-4.0.0.0.zip +echo export PATH=$install_path/gatk-4.0.0.0:\$PATH >> $source_file +} + + +#Rosetta +function install_Rosetta() { +yum -y install openssl-devel +pip3 install tensorflow nltk pandas +pip3 install tensorflow Rosetta +} + +#AlphaFold +function install_AlphaFold() { +pip3 install AlphaFold +} + +#STAR +function install_gatk() { +cd $install_path +wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.1a.tar.gz -O STAR-2.7.1a.tar.gz +tar -xvf STAR-2.7.1a.tar.gz && cd STAR-2.7.1a +sed -i 's/\?\=/\?= \-flto \-march=native \-mcpu=tsv110/g' source/Makefile|grep ? +cd source +make STAR +echo export PATH=$install_path/STAR-2.7.1a/source/:\$PATH >> $source_file +} + + + +#bgcc-10.3.1 +function install_gcc() { +cd $install_path +wget https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-10.3.1-2022.06-aarch64-linux.tar.gz +tar -xvf gcc-10.3.1-2022.06-aarch64-linux.tar.gz +cd gcc-10.3.1-2022.06-aarch64-linux +mkdir -p $targetdir/kunpeng-gcc-10.3.1 +cp -rf ./* $targetdir/kunpeng-gcc-10.3.1 +echo export PATH=$targetdir/kunpeng-gcc-10.3.1/bin:\$PATH >> $source_file +source $source_file +} + +#ncbi-vdb +function install_ncbi-vdb() { +cd $install_path +wget https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.0.tar.gz -O ncbi-vdb-3.0.0.tar.gz +yum -y install doxygen cmake +yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y +tar -xvf ncbi-vdb-3.0.0.tar.gz +cd ncbi-vdb-3.0.0 +cp -r interfaces/cc/gcc/arm64 interfaces/cc/gcc/aarch64 +./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 --prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 +make -j $(nproc) && make install +} + + +#sratoolkit-3.0.0 +function install_sratoolkit() { +install_ncbi-vdb +cd $install_path +wget https://github.com/ncbi/sra-tools/archive/refs/tags/3.0.0.tar.gz -O sratoolkit-3.0.0.tar.gz +yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y +tar zxvf sratoolkit-3.0.0.tar.gz +cd sra-tools-3.0.0 +cd tools/sharq/bm/ +wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/bmutil.h.patch + +patch -p0 < bmutil.h.patch +cd ../../../ +cd tools/copycat/ +wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/ccsra.c.patch +patch -p0 < ccsra.c.patch +cd ../../ +sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" tools/sharq/CMakeLists.txt +sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" test/sharq/CMakeLists.txt +cd tools/driver-tool/secure/ +wget https://gitee.com/openeuler/AvxToNeon/blob/master/avx2neon.h +sed -i 's/#include /#include /' string.cpp +cd ../../../ +./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --with-ncbi-vdb-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 +make -j $(nproc) +make install + +echo export $targetdir/sratoolkit/sra-tools-3.0.0/bin >> $source_file + +} + + +#cutadapt +function install_cutadapt() { +pip3 install cutadapt==4.1 +#pip3 install cutadapt -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com +} + + + +#Bowtie2 +function install_Bowtie2() { +cd $install_path +wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.4.1.tar.gz -O bowtie2-2.4.1.tar.gz +yum install zlib.aarch64 zlib-devel.aarch64 zlib-static.aarch64 +tar -xvf bowtie2-2.4.1.tar.gz +cd bowtie2-2.4.1 +mkdir -p third_party/simde/simde/x86/ +export NO_TBB=1 +export POPCNT_CAPABILITY=0 +wget https://codeload.github.com/simd-everywhere/simde/tar.gz/refs/tags/v0.7.6 -O simde-0.7.6.tar.gz +tar -xvf simde-0.7.6.tar.gz + +wget https://codeload.github.com/jratcliff63367/sse2neon/zip/refs/heads/master -O sse2neon.zip + +cp -a simde-0.7.6/simde third_party/simde/ +cp sse2neon-master/SSE2NEON.h sse2neon-master/sse2neon.h +cp -a sse2neon-master/sse2neon.h ./third_party/simde/simde/x86/ +make all +echo export PATH=$install_path/bowtie2-2.4.1:\$PATH >> $source_file +} + + + +#deeptool +function install_deeptool() { +cd $install_path +wget https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz -O deepTools-3.5.1.tar.gz +tar -xvf deepTools-3.5.1.tar.gz +cd $install_path/deepTools-3.5.1 +python3 setup.py install +} + + + +#meme +function install_meme() { +cd $install_path +wget https://meme-suite.org/meme/meme-software/5.4.0/meme-5.4.0.tar.gz +tar -xvf meme-5.4.0.tar.gz +cd meme-5.4.0 +yum install -y libtool* autoconf automake nodejs* perl* libxml2* libxslt* +#cpan XML::Simple +#cpan Sys::info +#cpan Math::CDF +#cpan HTML::TreeBuilder.pm +#cpan JSON +./configure --prefix=$targetdir/MEME +make +make install +echo export PATH=$targetdir/MEME/bin:\$PATH >> $source_file +} + + +#ncbi-blast +function install_ncbi-blast() { +cd $install_path +wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-src.tar.gz -O ncbi-blast-2.13.0+-src.tar.gz +tar xzf ncbi-blast-2.13.0+-src.tar.gz +cd ncbi-blast-2.13.0+-src +export BLAST_TOP=`pwd` +export CC=gcc +export CXX=g++ +cd $BLAST_TOP +tar -xvf LMDB_0.9.24.tar.gz +cd lmdb-LMDB_0.9.24 +export LMDB_PATH=$BLAST_TOP/lmdb-LMDB_0.9.24 +cd $BLAST_TOP/c++ +./configure +cd ReleaseMT/build +make all_r -j +make -j && make install +cd $BLAST_TOP/c++/ReleaseMT/bin +ls blastp +blastp +} + +#emboss +function install_emboss() { +cd $install_path +wget ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz +yum install -y epel-release +yum install -y gcc +yum install -y gcc-c++ +yum install -y cmake +yum install -y make +yum install -y libX11 +yum install -y libX11-devel +tar -zxvf EMBOSS-6.5.7.tar.gz +cd EMBOSS-6.5.7/ +./configure --prefix=$targetdir/EMBOSS --build=aarch64-unknown-linux-gnu +make -j +make install +cd $targetdir/EMBOSS/bin +echo export PATH=$targetdir/EMBOSS/bin:\$PATH >> $source_file +} + +# +function install_TRF() { +cd $install_path +#git clone https://github.com/Benson-Genomics-Lab/TRF.git +wget https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz -O TRF-4.09.1.tar.gz +tar -xvf TRF-4.09.1.tar.gz +cd TRF-4.09.1 +mkdir build +cd build +../configure --prefix=$targetdir/RepeatMasker/TRF_install +make -j +make install +} + +#ncbi-blast-2.10.0 +function install_ncbi-blast-2.10.0() { +cd $install_path +wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz +wget https://www.repeatmasker.org/rmblast/isb-2.10.0+-rmblast.patch.gz +tar -xvf ncbi-blast-2.10.0+-src.tar.gz +gunzip isb-2.10.0+-rmblast.patch.gz +cd ncbi-blast-2.10.0+-src +patch -p1 < ../isb-2.10.0+-rmblast.patch +cd c++ +wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/B_patch.cpp +patch $install_path/ncbi-blast-2.10.0+-src/c++/src/build-system/configure ./B_patch.cpp +./configure --with-mt --without-debug --without-krb5 --without-openssl --with-projects=scripts/projects/rmblastn/project.lst --prefix=$targetdir/rmblast/rmblast_install +make -j && make +make install +} + +#repeatmaster +function install_repeatmaster() { +install_TRF +install_ncbi-blast-2.10.0 + +yum install perl perl-CPAN -y +cd $install_path +wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz +tar -xvf RepeatMasker-4.1.2-p1.tar.gz +cd RepeatMasker +yum install python3 python3-pip pip3 install h5py +chmod -R 755 * +./configure + +#²$targetdirҪ滻ɱֵ +#$targetdir/RepeatMasker/TRF_install/bin/trf +# 2 +#$targetdir/rmblast/rmblast_install/bin/ +# y +#5 +echo export PATH=$install_path/RepeatMasker:\$PATH >> $source_file +} + + + +function install_bats-0.4.0() { +cd $install_path +wget https://github.com/sstephenson/bats/archive/refs/tags/v0.4.0.tar.gz +tar -xvf v0.4.0.tar.gz +cd bats-0.4.0 +echo export PATH=$install_path/bats-0.4.0/bin:\$PATH >> $source_file +} + +function install_pygtftk-1.6.2() { +install_bats-0.4.0 +cd $install_path +wget https://github.com/dputhier/pygtftk/archive/refs/tags/v1.6.2.tar.gz +tar xvf v1.6.2.tar.gz +cd pygtftk-1.6.2 +pip3 install -r requirements.txt +pip3 install cython==0.29.30 +python3 setup.py install +} + + +function install_python-3.11.5() { +cd $install_path +wget https://www.python.org/ftp/python/3.11.5/Python-3.11.5.tar.xz +tar xvf Python-3.11.5.tar.xz +cd Python-3.11.5 +./configure --prefix=$targetdir/python_3_11_5/python_3_11_5_install +make -j +make install +echo export PATH=$targetdir/python_3_11_5/python_3_11_5_install/bin:\$PATH >> $source_file +echo export LD_LIBRARY_PATH=$targetdir/python_3_11_5/python_3_11_5_install/lib:$LD_LIBRARY_PATH >> $source_file +echo export INCLUDE=/$targetdir/python_3_11_5/python_3_11_5_install/include:$INCLUDE >> $source_file +} + + +function install_snakemake-7.32.4() { +install_python-3.11.5 +install_BWA +install_samtools +cd $install_path +wget https://files.pythonhosted.org/packages/f4/94/884160dab89886cef7802df0a8c8217bfb2d795427dee01ad0e0dc15964a/snakemake-7.32.4.tar.gz +tar xvf v7.32.4.tar.gz +cd snakemake-7.32.4 +pip3 install . +} + +function install_lapack-3.8.0() { +cd $install_path +wget https://www.cp2k.org/static/downloads/lapack-3.8.0.tgz +tar xvf lapack-3.8.0.tgz +cd lapack-3.8.0 +cp make.inc.example make.inc +sed -i "23s/$/ -fallow-argument-mismatch/g" make.inc +sed -i "25s/$/ -fallow-argument-mismatch/g" make.inc +mkdir build +cd build +cmake .. -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$targetdir/lapack_3_8_0/lapack_3_8_0_install +make -j +make install +echo export LD_LIBRARY_PATH=$targetdir/lapack_3_8_0/lapack_3_8_0_install/lib:$LD_LIBRARY_PATH >> $source_file +} + +function install_R-4.3.0() { +install_lapack-3.8.0 +cd $install_path +wget https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz +tar xvf R-4.3.0.tar.gz +cd R-4.3.0 +yum install libXt-devel libX11-devel readline-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel libcurl-devel -y +./configure --prefix=$targetdir/R_4_3_0/R_4_3_0_install +make -j +make install +echo export PATH=$targetdir/R_4_3_0/R_4_3_0_install/bin:$PATH >> $source_file +echo export LD_LIBRARY_PATH=$targetdir/R_4_3_0/R_4_3_0_install/R/library:$LD_LIBRARY_PATH >> $source_file +} + +function install_scenic-1.3.1() { +install_R-4.3.0 +cd $install_path +R -e 'install.packages("BiocManager")' +R -e 'BiocManager::install("arrow")' +R -e 'install.packages("devtools")' +R -e 'devtools::install_github("aertslab/AUCell")' +R -e 'devtools::install_github("aertslab/RcisTarget")' +R -e 'devtools::install_github("aertslab/GENIE3")' +R -e 'BiocManager::install("ggrepel")' +R -e 'devtools::install_github("aertslab/SCENIC")' +} + +function install_seurat-5.0.0() { +install_R-4.3.0 +cd $install_path +wget https://github.com/satijalab/seurat/archive/refs/tags/v5.0.0.tar.gz +tar xvf v5.0.0.tar.gz +cd seurat-5.0.0/ +R -e 'install.packages("BiocManager")' +R -e 'BiocManager::install(c("SeuratObject", "cowplot", "fastDummies", "fitdistrplus", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "httr", "ica", "igraph", "irlba", "leiden", "lmtest", "matrixStats", "miniUI", "patchwork", "pbapply", "plotly", "png", "progressr", "RANN", "RColorBrewer", "RcppAnnoy", "RcppHNSW", "reticulate", "ROCR", "RSpectra", "Rtsne", "scales", "scattermore", "sctransform", "shiny", "spatstat.explore", "spatstat.geom", "tibble", "uwot", "RcppEigen", "RcppProgress"))' +R CMD INSTALL . +} + + +function install_reditools-2.0() { +cd $install_path +yum install environment-modules openmpi-devel -y +source /etc/profile +module load mpi/openmpi-aarch64 +git clone https://github.com/tizianoflati/reditools2.0 +cd reditools2.0 +pip3 install -r requirements.txt +} + +#װopenblas +function install_openblas() { +cd $install_path +wget https://github.com/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz +tar -xvf OpenBLAS-0.3.23.tar.gz +cd OpenBLAS-0.3.23 +make -j 16 ARCH=aarch64 all +make PREFIX=$targetdir/openblas/openblas_install install +echo export PATH=$targetdir/openblas/openblas_install/bin:\$PATH >> $source_file +echo export LD_LIBRARY_PATH=$targetdir/openblas/openblas_install/lib:\$LD_LIBRARY_PATH >> $source_file +} + +#װgsl +function install_gsl() { +cd $install_path +wget https://ftpmirror.gnu.org/gsl/gsl-2.7.1.tar.gz +tar -xf gsl-2.7.1.tar.gz +cd gsl-2.7.1/ +./configure --prefix=$targetdir/gsl/gsl_install +make -j 16 +make install +echo export PATH=$targetdir/gsl/gsl_install/bin:\$PATH >> $source_file +echo export LD_LIBRARY_PATH=$targetdir/gsl/gsl_install/lib:\$LD_LIBRARY_PATH >> $source_file +} + +#װadmixtools +function install_admixtools() { +#װopenblas +install_openblas +#װgsl +install_gsl +cd $install_path +wget https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz +tar -xf v7.0.2.tar.gz +cd AdmixTools-7.0.2/src +sed -i '14d' Makefile +sed -i '18d' Makefile +sed -i "14s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile +sed -i "15s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install +mkdir -p $targetdir/admixtools/admixtools_install +cp -r ../bin $targetdir/admixtools/admixtools_install/bin +echo export PATH=$targetdir/admixtools/admixtools_install/bin:\$PATH >> $source_file +} + +#װEIG +function install_EIG() { +#װopenblas +install_openblas +#װgsl +install_gsl +cd $install_path +wget https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz +mv v8.0.0.tar.gz EIG-8.0.0.tar.gz +tar -xf EIG-8.0.0.tar.gz +cd EIG-8.0.0/src +sed -i "1s%^.*$%override CFLAGS += -I../include -I$targetdir/openblas/openblas_install/include%g" Makefile +sed -i '10d' Makefile +sed -i '12d' Makefile +sed -i "10s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile +sed -i "11s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install +mkdir -p $targetdir/EIG/EIG_install +cp -r ../bin $targetdir/EIG/EIG_install +cp -r ../include $targetdir/EIG_install +echo export PATH=$targetdir/EIG_install/bin:\$PATH >> $source_file +} + +#װgdal +function install_gadl() { +cd $install_path +yum install proj proj-devel -y +wget https://download.osgeo.org/gdal/3.7.0/gdal-3.7.0.tar.xz +tar -xf gdal-3.7.0.tar.xz +cd gdal-3.7.0/ +mkdir build +cd build +cmake ../ -DCMAKE_INSTALL_PREFIX=$targetdir/gdal/gdal_install +make install +echo export PATH=$targetdir/gdal/gdal_install/bin:\$PATH >> $source_file +echo export LD_LIBRARY_PATH=$targetdir/gdal/gdal_install/lib:\$LD_LIBRARY_PATH >> $source_file +} + +#װcommot +function install_commot() { +#װ +yum install python3-devel python3 python3-pip git make -y +install_gadl +source $source_file +pip install commot -i https://pypi.tuna.tsinghua.edu.cn/simple +} + + + + +if [ ! -n "$OPT" ]; then +install_$OPT +else +source $source_file +fi \ No newline at end of file diff --git a/package/ncbi-vdb/3.0.0/install.sh b/package/ncbi-vdb/3.0.0/install.sh new file mode 100644 index 0000000..614821d --- /dev/null +++ b/package/ncbi-vdb/3.0.0/install.sh @@ -0,0 +1,15 @@ +#!/bin/bash +set -x +set -e + +wget https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.0.tar.gz -O ${JARVIS_DOWNLOAD}/ncbi-vdb-3.0.0.tar.gz +yum -y install doxygen cmake +yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/ncbi-vdb-3.0.0.tar.gz + +cd ncbi-vdb-3.0.0 +cp -r interfaces/cc/gcc/arm64 interfaces/cc/gcc/aarch64 +./configure --relative-build-out-dir +make -j && make install diff --git a/proxy.sh b/proxy.sh index a1d3ff0..80620c8 100644 --- a/proxy.sh +++ b/proxy.sh @@ -38,5 +38,5 @@ elif [[ $aNum -eq 'b' ]]; then cp src/dataService.py.ori src/dataService.py export UseGitee=0 else - echo '无效输入，请输入 1 到 7 之间的数字' + echo '无效输入，请输入 1~6|a,b 之间的数字' fi \ No newline at end of file -- Gitee From 3eb1aefd4d599e0a1f8c076643a8495be287a618 Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Wed, 4 Dec 2024 20:18:28 +0800 Subject: [PATCH 5/7] update package --- package/R/4.3.0/install.sh | 16 +++ package/admixtools/7.0.2/install.sh | 15 +++ package/blat/35.1/install.sh | 13 +++ package/gcc/10.3.1/install.sh | 7 ++ package/gcc/12.3.1/install.sh | 7 ++ package/lifescience/install.sh | 157 ---------------------------- package/samtools/1.15/install.sh | 8 +- 7 files changed, 63 insertions(+), 160 deletions(-) create mode 100644 package/R/4.3.0/install.sh create mode 100644 package/admixtools/7.0.2/install.sh create mode 100644 package/blat/35.1/install.sh create mode 100644 package/gcc/10.3.1/install.sh create mode 100644 package/gcc/12.3.1/install.sh diff --git a/package/R/4.3.0/install.sh b/package/R/4.3.0/install.sh new file mode 100644 index 0000000..5f90662 --- /dev/null +++ b/package/R/4.3.0/install.sh @@ -0,0 +1,16 @@ +#!/bin/bash +set -x +set -e + +. $CHECK_ROOT +yum install libXt-devel.aarch64 readline-devel.aarch64 -y +yum install libX11-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel libcurl-devel -y + +. ${DOWNLOAD_TOOL} -u https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz + +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/R-4.3.0.tar.gz +cd R-4.3.0 +./configure -enable-R-shlib -enable-R-static-lib --with-libpng --with-jpeglib --prefix=$1 +make all -j +make install diff --git a/package/admixtools/7.0.2/install.sh b/package/admixtools/7.0.2/install.sh new file mode 100644 index 0000000..2acdbbd --- /dev/null +++ b/package/admixtools/7.0.2/install.sh @@ -0,0 +1,15 @@ +#!/bin/bash +set -x +set -e + +wget https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz -O ${JARVIS_DOWNLOAD}/AdmixTools-7.0.2.tar.gz + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/AdmixTools-7.0.2.tar.gz +cd AdmixTools-7.0.2/src +sed -i '14d' Makefile +sed -i '18d' Makefile +sed -i "14s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile +sed -i "15s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile +make -j 16 +make install \ No newline at end of file diff --git a/package/blat/35.1/install.sh b/package/blat/35.1/install.sh new file mode 100644 index 0000000..fddc861 --- /dev/null +++ b/package/blat/35.1/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash +set -x +set -e + +wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1 -O ${JARVIS_DOWNLOAD}/blat-35.1.tar.gz +yum -y install libpng-devel + +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/blat-35.1.tar.gz +cd blat-35.1/ +sed -i 's/jmp_buf htmlRecover/\/\/jmp_buf htmlRecover/g' src/inc/htmshell.h +export MACHTYPE=aarch64 +make \ No newline at end of file diff --git a/package/gcc/10.3.1/install.sh b/package/gcc/10.3.1/install.sh new file mode 100644 index 0000000..a35f403 --- /dev/null +++ b/package/gcc/10.3.1/install.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-10.3.1-2022.06-aarch64-linux.tar.gz +cd ${JARVIS_TMP} +rm -rf gcc-10.3.1 +tar -xzvf ${JARVIS_DOWNLOAD}/gcc-10.3.1-2022.06-aarch64-linux.tar.gz \ No newline at end of file diff --git a/package/gcc/12.3.1/install.sh b/package/gcc/12.3.1/install.sh new file mode 100644 index 0000000..ef3aed6 --- /dev/null +++ b/package/gcc/12.3.1/install.sh @@ -0,0 +1,7 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-12.3.1-2024.09-aarch64-linux.tar.gz +cd ${JARVIS_TMP} +rm -rf gcc-12.3.1 +tar -xzvf ${JARVIS_DOWNLOAD}/gcc-12.3.1-2024.09-aarch64-linux.tar.gz \ No newline at end of file diff --git a/package/lifescience/install.sh b/package/lifescience/install.sh index f22ecb4..175b65c 100644 --- a/package/lifescience/install.sh +++ b/package/lifescience/install.sh @@ -77,59 +77,11 @@ make echo export PATH=$install_path/randfold/src >> $source_file } -#blat -function install_BLAT() { -cd $install_path -wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1 -O blat-35.1.tar.gz -yum -y install libpng-devel -tar zxvf blat-35.1.tar.gz -cd blat-35.1/ -sed -i 's/jmp_buf htmlRecover/\/\/jmp_buf htmlRecover/g' src/inc/htmshell.h -export MACHTYPE=aarch64 -make -echo export PATH=$install_path/blat-35.1/bin:\$PATH >> $source_file -} -#BWA -function install_BWA() { -cd $install_path -wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 -tar -xvf bwa-0.7.17.tar.bz2 -cd bwa-0.7.17 && wget https://raw.githubusercontent.com/jratcliff63367/sse2neon/master/SSE2NEON.h -sed -i 's/#include /#include "SSE2NEON.h"/g' ksw.c -sed -i 's/const uint8_t rle_auxtab/\/\/const uint8_t rle_auxtab/g' rle.h |grep rle_auxtab -make -echo export PATH=$install_path/bwa-0.7.17:\$PATH >> $source_file -} -#samtools -function install_samtools() { -#gcc-10.3.1 -cd $install_path -wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O samtools-0.1.9.tar.gz -tar -xvf samtools-0.1.9.tar.gz -cd samtools-0.1.9 -make -echo export PATH=$install_path/samtools-0.1.9:\$PATH >> $source_file -} -#gatk -function install_gatk() { -#blat,bwa -#blat -install_BLAT -#BWA -install_BWA -#samtools -install_samtools -cd $install_path -wget https://github.com/broadinstitute/gatk/releases/download/4.0.0.0/gatk-4.0.0.0.zip -O gatk-4.0.0.0.zip -unzip gatk-4.0.0.0.zip -echo export PATH=$install_path/gatk-4.0.0.0:\$PATH >> $source_file -} - #Rosetta function install_Rosetta() { @@ -155,19 +107,6 @@ echo export PATH=$install_path/STAR-2.7.1a/source/:\$PATH >> $source_file } - -#bgcc-10.3.1 -function install_gcc() { -cd $install_path -wget https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-10.3.1-2022.06-aarch64-linux.tar.gz -tar -xvf gcc-10.3.1-2022.06-aarch64-linux.tar.gz -cd gcc-10.3.1-2022.06-aarch64-linux -mkdir -p $targetdir/kunpeng-gcc-10.3.1 -cp -rf ./* $targetdir/kunpeng-gcc-10.3.1 -echo export PATH=$targetdir/kunpeng-gcc-10.3.1/bin:\$PATH >> $source_file -source $source_file -} - #ncbi-vdb function install_ncbi-vdb() { cd $install_path @@ -436,19 +375,6 @@ make install echo export LD_LIBRARY_PATH=$targetdir/lapack_3_8_0/lapack_3_8_0_install/lib:$LD_LIBRARY_PATH >> $source_file } -function install_R-4.3.0() { -install_lapack-3.8.0 -cd $install_path -wget https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz -tar xvf R-4.3.0.tar.gz -cd R-4.3.0 -yum install libXt-devel libX11-devel readline-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel libcurl-devel -y -./configure --prefix=$targetdir/R_4_3_0/R_4_3_0_install -make -j -make install -echo export PATH=$targetdir/R_4_3_0/R_4_3_0_install/bin:$PATH >> $source_file -echo export LD_LIBRARY_PATH=$targetdir/R_4_3_0/R_4_3_0_install/R/library:$LD_LIBRARY_PATH >> $source_file -} function install_scenic-1.3.1() { install_R-4.3.0 @@ -485,90 +411,7 @@ cd reditools2.0 pip3 install -r requirements.txt } -#װopenblas -function install_openblas() { -cd $install_path -wget https://github.com/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz -tar -xvf OpenBLAS-0.3.23.tar.gz -cd OpenBLAS-0.3.23 -make -j 16 ARCH=aarch64 all -make PREFIX=$targetdir/openblas/openblas_install install -echo export PATH=$targetdir/openblas/openblas_install/bin:\$PATH >> $source_file -echo export LD_LIBRARY_PATH=$targetdir/openblas/openblas_install/lib:\$LD_LIBRARY_PATH >> $source_file -} -#װgsl -function install_gsl() { -cd $install_path -wget https://ftpmirror.gnu.org/gsl/gsl-2.7.1.tar.gz -tar -xf gsl-2.7.1.tar.gz -cd gsl-2.7.1/ -./configure --prefix=$targetdir/gsl/gsl_install -make -j 16 -make install -echo export PATH=$targetdir/gsl/gsl_install/bin:\$PATH >> $source_file -echo export LD_LIBRARY_PATH=$targetdir/gsl/gsl_install/lib:\$LD_LIBRARY_PATH >> $source_file -} - -#װadmixtools -function install_admixtools() { -#װopenblas -install_openblas -#װgsl -install_gsl -cd $install_path -wget https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz -tar -xf v7.0.2.tar.gz -cd AdmixTools-7.0.2/src -sed -i '14d' Makefile -sed -i '18d' Makefile -sed -i "14s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile -sed -i "15s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile -make -j 16 -make install -mkdir -p $targetdir/admixtools/admixtools_install -cp -r ../bin $targetdir/admixtools/admixtools_install/bin -echo export PATH=$targetdir/admixtools/admixtools_install/bin:\$PATH >> $source_file -} - -#װEIG -function install_EIG() { -#װopenblas -install_openblas -#װgsl -install_gsl -cd $install_path -wget https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz -mv v8.0.0.tar.gz EIG-8.0.0.tar.gz -tar -xf EIG-8.0.0.tar.gz -cd EIG-8.0.0/src -sed -i "1s%^.*$%override CFLAGS += -I../include -I$targetdir/openblas/openblas_install/include%g" Makefile -sed -i '10d' Makefile -sed -i '12d' Makefile -sed -i "10s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile -sed -i "11s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile -make -j 16 -make install -mkdir -p $targetdir/EIG/EIG_install -cp -r ../bin $targetdir/EIG/EIG_install -cp -r ../include $targetdir/EIG_install -echo export PATH=$targetdir/EIG_install/bin:\$PATH >> $source_file -} - -#װgdal -function install_gadl() { -cd $install_path -yum install proj proj-devel -y -wget https://download.osgeo.org/gdal/3.7.0/gdal-3.7.0.tar.xz -tar -xf gdal-3.7.0.tar.xz -cd gdal-3.7.0/ -mkdir build -cd build -cmake ../ -DCMAKE_INSTALL_PREFIX=$targetdir/gdal/gdal_install -make install -echo export PATH=$targetdir/gdal/gdal_install/bin:\$PATH >> $source_file -echo export LD_LIBRARY_PATH=$targetdir/gdal/gdal_install/lib:\$LD_LIBRARY_PATH >> $source_file -} #װcommot function install_commot() { diff --git a/package/samtools/1.15/install.sh b/package/samtools/1.15/install.sh index cbfaae6..8479ba0 100755 --- a/package/samtools/1.15/install.sh +++ b/package/samtools/1.15/install.sh @@ -1,8 +1,10 @@ #!/bin/bash set -x set -e -wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O ${JARVIS_TMP}/samtools-0.1.9.tar.gz +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 cd ${JARVIS_TMP} -tar xvf ${JARVIS_DOWNLOAD}/samtools-0.1.9.tar.gz -cd samtools-0.1.9 +tar xvf ${JARVIS_DOWNLOAD}/samtools-1.15.tar.bz2 +cd samtools-1.15 +./configure --prefix=$1 make -j +make install \ No newline at end of file -- Gitee From b25999048eaa41448d61623b24fe0a5f020f0118 Mon Sep 17 00:00:00 2001 From: sunlock0653 Date: Wed, 4 Dec 2024 21:14:22 +0800 Subject: [PATCH 6/7] update life science --- package/lifescience/install.sh | 1598 +++++++++++++++++++++++++++++++ package/octopus/11.4/install.sh | 155 +++ 2 files changed, 1753 insertions(+) create mode 100644 package/octopus/11.4/install.sh diff --git a/package/lifescience/install.sh b/package/lifescience/install.sh index 175b65c..b045a80 100644 --- a/package/lifescience/install.sh +++ b/package/lifescience/install.sh @@ -424,9 +424,1607 @@ pip install commot -i https://pypi.tuna.tsinghua.edu.cn/simple +#!/bin/bash + +#ѧ װʹܽűҪװrandfoldִ +# sh hpc_life_science.sh randfold +#ʹӦִ +#sh hpc_life_science.sh + +#--------------------------------# +OPT=$1; + +##ȫֱ +#--------------------------------# +passwd=123456; +install_path=/home/sunqian +targetdir=$install_path/BIN +source_file=$install_path/source_sun.sh +cpu_num=`grep -c "processor" /proc/cpuinfo`; #CPU +netcard=`cat /proc/net/dev|sort -rn -k2|awk '{print $1}'|awk NR==1|awk -F ':' '{print $1}'`;# +ip_addr=`ip a|grep $netcard|grep inet|awk '{print $2}'|awk -F '/' '{print $1}'` #ipַ +osType=`cat /etc/os-release|grep ID |awk NR==1|awk -F \" '{print $2}'` +basearch=`arch` + + + +#--------------------------------# +mkdir -p $targetdir +echo install_path=$install_path >> $source_file +touch $source_file + + +#--------------------------------# +#ȫ +cd $install_path +yum -y install make gcc g++ git +yum install -y java-1.8.0-openjdk-devel.aarch64 ncurses-devel.aarch64 bzip2-devel.aarch64 python3-devel python bazel cmake3 +pip3 install tensorflow + + +function install_R-4.3.0() { + install_lapack-3.8.0 + cd $install_path + wget https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz + tar xvf R-4.3.0.tar.gz + cd R-4.3.0 + yum install libXt-devel libX11-devel readline-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel libcurl-devel -y + ./configure --prefix=$targetdir/R_4_3_0/R_4_3_0_install + make -j + make install + echo export PATH=$targetdir/R_4_3_0/R_4_3_0_install/bin:$PATH >> $source_file + echo export LD_LIBRARY_PATH=$targetdir/R_4_3_0/R_4_3_0_install/R/library:$LD_LIBRARY_PATH >> $source_file +} + +#GSEA +function install_GSEA() { + #װjava + yum install java-11-openjdk-devel.aarch64 -y + #װӻ + #yum install xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -y + #sed -i "s/X11Forwarding no/X11Forwarding yes/g" /etc/ssh/sshd_config + #systemctl restart sshd.service + cd $install_path + wget https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip + unzip GSEA_4.3.2.zip + echo export PATH=$install_path/GSEA_4.3.2:\$PATH >> $source_file +} + +#pangolin +function install_pangolin() { + #װ + yum install python3-devel python3 python3-pip git make -y + cd $install_path + wget https://github.com/cov-lineages/pangolin/archive/refs/tags/v4.3.1.tar.gz -O pangolin-v4.3.1.tar.gz + tar xf pangolin-v4.3.1.tar.gz + cd pangolin-4.3.1 + pip3 install . -i https://pypi.tuna.tsinghua.edu.cn/simple + pip3 install git+https://github.com/cov-lineages/pangolin-data.git + pip3 install git+https://github.com/cov-lineages/scorpio.git + pip3 install git+https://github.com/cov-lineages/constellations.git + pip3 install snakemake -i https://pypi.tuna.tsinghua.edu.cn/simple +} + + + +#randfold +function install_randfold() { + cd $install_path + git clone https://github.com/eb00/randfold.git + cd randfold/src/squid-1.9g + ./configure && make + cd ../ + make + echo export PATH=$install_path/randfold/src >> $source_file + } + + #blat + function install_BLAT() { + cd $install_path + wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1 -O blat-35.1.tar.gz + yum -y install libpng-devel + tar zxvf blat-35.1.tar.gz + cd blat-35.1/ + sed -i 's/jmp_buf htmlRecover/\/\/jmp_buf htmlRecover/g' src/inc/htmshell.h + export MACHTYPE=aarch64 + make + echo export PATH=$install_path/blat-35.1/bin:\$PATH >> $source_file +} + + +#BWA +function install_BWA() { + cd $install_path + wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 + tar -xvf bwa-0.7.17.tar.bz2 + cd bwa-0.7.17 && wget https://raw.githubusercontent.com/jratcliff63367/sse2neon/master/SSE2NEON.h + sed -i 's/#include /#include "SSE2NEON.h"/g' ksw.c + sed -i 's/const uint8_t rle_auxtab/\/\/const uint8_t rle_auxtab/g' rle.h |grep rle_auxtab + make + echo export PATH=$install_path/bwa-0.7.17:\$PATH >> $source_file +} + + + +#gatk +function install_gatk() { + #blat,bwa + #blat + install_BLAT + #BWA + install_BWA + #samtools + install_samtools + cd $install_path + wget https://github.com/broadinstitute/gatk/releases/download/4.0.0.0/gatk-4.0.0.0.zip -O gatk-4.0.0.0.zip + unzip gatk-4.0.0.0.zip + echo export PATH=$install_path/gatk-4.0.0.0:\$PATH >> $source_file +} + + +#Rosetta +function install_Rosetta() { + yum -y install openssl-devel + pip3 install tensorflow nltk pandas + pip3 install tensorflow Rosetta +} + +#AlphaFold +function install_AlphaFold() { + pip3 install AlphaFold +} + +#STAR +function install_star() { + cd $install_path + wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.1a.tar.gz -O STAR-2.7.1a.tar.gz + tar -xvf STAR-2.7.1a.tar.gz && cd STAR-2.7.1a + sed -i 's/\?\=/\?= \-flto \-march=native \-mcpu=tsv110/g' source/Makefile|grep ? + cd source + make STAR + echo export PATH=$install_path/STAR-2.7.1a/source/:\$PATH >> $source_file +} + +function install_gcc-9.3.1() { +#bgcc +mkdir -p $install_path/gcc +cd $install_path +wget http://mirrors.concertpass.com/gcc/releases/gcc-9.1.0/gcc-9.1.0.tar.xz +wget gcc.gnu.org/pub/gcc/infrastructure/gmp-6.1.0.tar.bz2 +wget gcc.gnu.org/pub/gcc/infrastructure/mpfr-3.1.4.tar.bz2 +wget gcc.gnu.org/pub/gcc/infrastructure/mpc-1.0.3.tar.gz +wget gcc.gnu.org/pub/gcc/infrastructure/isl-0.18.tar.bz2 + + + +#gccgmpmpfrmpcislĸ⣬mpfrgmpislgmpmpcgmpmpfr˰װgcc֮ǰȸϵΰװĸ + +tar -xvf gcc-9.1.0.tar.xz +tar -xvf gmp-6.1.0.tar.bz2 +tar -xvf mpfr-3.1.4.tar.bz2 +tar -xvf mpc-1.0.3.tar.gz +tar -xvf mpc-1.0.3.tar.gz + + +#װgmp +cd $install_path/gmp-6.1.0 +./configure --prefix=$install_path/gcc/gmp-6.1.2 +make -j64 && make install +cd .. + + +#װmpfr +cd $install_path/mpfr-3.1.4 +./configure --prefix=$install_path/gcc/mpfr-3.1.4 --with-gmp=$install_path/gcc/gmp-6.1.2 +make -j64 && make install +cd .. + +#װmpc +cd $install_path/mpc-1.0.3 +./configure --prefix=$install_path/gcc/mpc-1.0.3 --with-gmp=$install_path/gcc/gmp-6.1.2 --with-mpfr=$install_path/gcc/mpfr-3.1.4 +make -j64 && make install +cd .. + +#װisl +yum -y install gmp-devel +cd $install_path/isl-0.18 +./configure --prefix=$install_path/gcc/isl-0.18 --with-gmp=$install_path/gcc/gmp-6.1.2 --with-mpfr=$install_path/gcc/mpfr-3.1.4 --with-mpc=$install_path/gcc/mpc-1.0.3 +make -j64 && make install +cd .. + +cd $install_path/gcc-9.1.0 +mkdir gcc-build-9.1.0 +cd gcc-build-9.1.0 +rm -rf ../host-aarch64-unknown-linux-gnu +../configure --enable-checking=release --enable-languages=c,c++ --disable-multilib --prefix=$install_path/gcc/gcc-9.1.0 --with-gmp=$install_path/gcc/gmp-6.1.2 --with-mpfr=$install_path/gcc/mpfr-3.1.4 --with-mpc=$install_path/gcc/mpc-1.0.3 +make -j64 && make install +echo export PATH=$install_path/gcc/gcc-9.1.0/bin/:\$PATH >> $source_file + + +g++ --version +} + +#bgcc-10.3.1 +function install_gcc() { + cd $install_path + wget https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-10.3.1-2022.06-aarch64-linux.tar.gz + tar -xvf gcc-10.3.1-2022.06-aarch64-linux.tar.gz + cd gcc-10.3.1-2022.06-aarch64-linux + mkdir -p $targetdir/kunpeng-gcc-10.3.1 + cp -rf ./* $targetdir/kunpeng-gcc-10.3.1 + echo export PATH=$targetdir/kunpeng-gcc-10.3.1/bin:\$PATH >> $source_file + source $source_file +} + + +function install_go() { + cd $targetdir + wget https://golang.google.cn/dl/go1.18.2.linux-arm64.tar.gz + mkdir -p go_install + mv go1.18.2.linux-arm64.tar.gz ./go_install + + cd ./go_install + tar -xf go1.18.2.linux-arm64.tar.gz + yum install environment-modules -y + source /etc/profile + cat > $targetdir/go_install/go_modulefiles << EOF +#%Module1.0 +conflict go +variable modfile [file normalize [info script]] +proc getModulefileDir {} { + variable modfile + set modfile_path [file dirname $modfile] + return $modfile_path +} +set pwd [getModulefileDir] +set GO_install $pwd +setenv GO_install $GO_install +prepend-path PATH $GO_install/go/bin + +EOF + module use /usr/local/go_install/ + module load /usr/local/go_install/go_modulefiles + go version + +} + +#ncbi-vdb +function install_ncbi-vdb() { + cd $install_path + wget https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.0.tar.gz -O ncbi-vdb-3.0.0.tar.gz + yum -y install doxygen cmake + yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y + tar -xvf ncbi-vdb-3.0.0.tar.gz + cd ncbi-vdb-3.0.0 + cp -r interfaces/cc/gcc/arm64 interfaces/cc/gcc/aarch64 + ./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 --prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 + make -j $(nproc) && make install +} + + +#sratoolkit-3.0.0 +function install_sratoolkit() { + install_ncbi-vdb + cd $install_path + wget https://github.com/ncbi/sra-tools/archive/refs/tags/3.0.0.tar.gz -O sratoolkit-3.0.0.tar.gz + yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y + tar zxvf sratoolkit-3.0.0.tar.gz + cd sra-tools-3.0.0 + cd tools/sharq/bm/ + wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/bmutil.h.patch + + patch -p0 < bmutil.h.patch + cd ../../../ + cd tools/copycat/ + wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/ccsra.c.patch + patch -p0 < ccsra.c.patch + cd ../../ + sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" tools/sharq/CMakeLists.txt + sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" test/sharq/CMakeLists.txt + cd tools/driver-tool/secure/ + wget https://gitee.com/openeuler/AvxToNeon/blob/master/avx2neon.h + sed -i 's/#include /#include /' string.cpp + cd ../../../ + ./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --with-ncbi-vdb-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 + make -j $(nproc) + make install + + echo export $targetdir/sratoolkit/sra-tools-3.0.0/bin >> $source_file + +} + + +#cutadapt +function install_cutadapt() { + pip3 install cutadapt==4.1 + #pip3 install cutadapt -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com +} + + + +#Bowtie2 +function install_Bowtie2() { + cd $install_path + wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.4.1.tar.gz -O bowtie2-2.4.1.tar.gz + yum install zlib.aarch64 zlib-devel.aarch64 zlib-static.aarch64 + tar -xvf bowtie2-2.4.1.tar.gz + cd bowtie2-2.4.1 + mkdir -p third_party/simde/simde/x86/ + export NO_TBB=1 + export POPCNT_CAPABILITY=0 + wget https://codeload.github.com/simd-everywhere/simde/tar.gz/refs/tags/v0.7.6 -O simde-0.7.6.tar.gz + tar -xvf simde-0.7.6.tar.gz + + wget https://codeload.github.com/jratcliff63367/sse2neon/zip/refs/heads/master -O sse2neon.zip + + cp -a simde-0.7.6/simde third_party/simde/ + cp sse2neon-master/SSE2NEON.h sse2neon-master/sse2neon.h + cp -a sse2neon-master/sse2neon.h ./third_party/simde/simde/x86/ + make all + echo export PATH=$install_path/bowtie2-2.4.1:\$PATH >> $source_file +} + + + +#deeptool +function install_deeptool() { + cd $install_path + wget https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz -O deepTools-3.5.1.tar.gz + tar -xvf deepTools-3.5.1.tar.gz + cd $install_path/deepTools-3.5.1 + python3 setup.py install +} + + + +#meme +function install_meme() { + cd $install_path + wget https://meme-suite.org/meme/meme-software/5.4.0/meme-5.4.0.tar.gz + tar -xvf meme-5.4.0.tar.gz + cd meme-5.4.0 + yum install -y libtool* autoconf automake nodejs* perl* libxml2* libxslt* + #cpan XML::Simple + #cpan Sys::info + #cpan Math::CDF + #cpan HTML::TreeBuilder.pm + #cpan JSON + ./configure --prefix=$targetdir/MEME + make + make install + echo export PATH=$targetdir/MEME/bin:\$PATH >> $source_file +} + + +#ncbi-blast +function install_ncbi-blast() { + cd $install_path + wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-src.tar.gz -O ncbi-blast-2.13.0+-src.tar.gz + tar xzf ncbi-blast-2.13.0+-src.tar.gz + cd ncbi-blast-2.13.0+-src + export BLAST_TOP=`pwd` + export CC=gcc + export CXX=g++ + cd $BLAST_TOP + tar -xvf LMDB_0.9.24.tar.gz + cd lmdb-LMDB_0.9.24 + export LMDB_PATH=$BLAST_TOP/lmdb-LMDB_0.9.24 + cd $BLAST_TOP/c++ + ./configure + cd ReleaseMT/build + make all_r -j + make -j && make install + cd $BLAST_TOP/c++/ReleaseMT/bin + ls blastp + blastp +} + +#emboss +function install_emboss() { + cd $install_path + wget ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz + yum install -y epel-release + yum install -y gcc + yum install -y gcc-c++ + yum install -y cmake + yum install -y make + yum install -y libX11 + yum install -y libX11-devel + tar -zxvf EMBOSS-6.5.7.tar.gz + cd EMBOSS-6.5.7/ + ./configure --prefix=$targetdir/EMBOSS --build=aarch64-unknown-linux-gnu + make -j + make install + cd $targetdir/EMBOSS/bin + echo export PATH=$targetdir/EMBOSS/bin:\$PATH >> $source_file +} + +# +function install_TRF() { + cd $install_path + #git clone https://github.com/Benson-Genomics-Lab/TRF.git + wget https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz -O TRF-4.09.1.tar.gz + tar -xvf TRF-4.09.1.tar.gz + cd TRF-4.09.1 + mkdir build + cd build + ../configure --prefix=$targetdir/RepeatMasker/TRF_install + make -j + make install +} + +#ncbi-blast-2.10.0 +function install_ncbi-blast-2.10.0() { + cd $install_path + wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz + wget https://www.repeatmasker.org/rmblast/isb-2.10.0+-rmblast.patch.gz + tar -xvf ncbi-blast-2.10.0+-src.tar.gz + gunzip isb-2.10.0+-rmblast.patch.gz + cd ncbi-blast-2.10.0+-src + patch -p1 < ../isb-2.10.0+-rmblast.patch + cd c++ + wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/B_patch.cpp + patch $install_path/ncbi-blast-2.10.0+-src/c++/src/build-system/configure ./B_patch.cpp + ./configure --with-mt --without-debug --without-krb5 --without-openssl --with-projects=scripts/projects/rmblastn/project.lst --prefix=$targetdir/rmblast/rmblast_install + make -j && make + make install +} + +#repeatmaster +function install_repeatmaster() { + install_TRF + install_ncbi-blast-2.10.0 + + yum install perl perl-CPAN -y + cd $install_path + wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz + tar -xvf RepeatMasker-4.1.2-p1.tar.gz + cd RepeatMasker + yum install python3 python3-pip pip3 install h5py + chmod -R 755 * + ./configure + + #²$targetdirҪ滻ɱֵ + #$targetdir/RepeatMasker/TRF_install/bin/trf + # 2 + #$targetdir/rmblast/rmblast_install/bin/ + # y + #5 + echo export PATH=$install_path/RepeatMasker:\$PATH >> $source_file +} + + + +function install_bats-0.4.0() { + cd $install_path + wget https://github.com/sstephenson/bats/archive/refs/tags/v0.4.0.tar.gz + tar -xvf v0.4.0.tar.gz + cd bats-0.4.0 + echo export PATH=$install_path/bats-0.4.0/bin:\$PATH >> $source_file +} + +function install_pygtftk-1.6.2() { + install_bats-0.4.0 + cd $install_path + wget https://github.com/dputhier/pygtftk/archive/refs/tags/v1.6.2.tar.gz + tar xvf v1.6.2.tar.gz + cd pygtftk-1.6.2 + pip3 install -r requirements.txt + pip3 install cython==0.29.30 + python3 setup.py install +} + + +function install_python-3.11.5() { + cd $install_path + wget https://www.python.org/ftp/python/3.11.5/Python-3.11.5.tar.xz + tar xvf Python-3.11.5.tar.xz + cd Python-3.11.5 + ./configure --prefix=$targetdir/python_3_11_5/python_3_11_5_install + make -j + make install + echo export PATH=$targetdir/python_3_11_5/python_3_11_5_install/bin:\$PATH >> $source_file + echo export LD_LIBRARY_PATH=$targetdir/python_3_11_5/python_3_11_5_install/lib:$LD_LIBRARY_PATH >> $source_file + echo export INCLUDE=/$targetdir/python_3_11_5/python_3_11_5_install/include:$INCLUDE >> $source_file +} + + +function install_snakemake-7.32.4() { + install_python-3.11.5 + install_BWA + install_samtools + cd $install_path + wget https://files.pythonhosted.org/packages/f4/94/884160dab89886cef7802df0a8c8217bfb2d795427dee01ad0e0dc15964a/snakemake-7.32.4.tar.gz + tar xvf v7.32.4.tar.gz + cd snakemake-7.32.4 + pip3 install . +} + +function install_lapack-3.8.0() { + cd $install_path + wget https://www.cp2k.org/static/downloads/lapack-3.8.0.tgz + tar xvf lapack-3.8.0.tgz + cd lapack-3.8.0 + cp make.inc.example make.inc + sed -i "23s/$/ -fallow-argument-mismatch/g" make.inc + sed -i "25s/$/ -fallow-argument-mismatch/g" make.inc + mkdir build + cd build + cmake .. -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$targetdir/lapack_3_8_0/lapack_3_8_0_install + make -j + make install + echo export LD_LIBRARY_PATH=$targetdir/lapack_3_8_0/lapack_3_8_0_install/lib:$LD_LIBRARY_PATH >> $source_file +} + + + +function install_scenic-1.3.1() { + install_R-4.3.0 + cd $install_path + R -e 'install.packages("BiocManager")' + R -e 'BiocManager::install("arrow")' + R -e 'install.packages("devtools")' + R -e 'devtools::install_github("aertslab/AUCell")' + R -e 'devtools::install_github("aertslab/RcisTarget")' + R -e 'devtools::install_github("aertslab/GENIE3")' + R -e 'BiocManager::install("ggrepel")' + R -e 'devtools::install_github("aertslab/SCENIC")' +} + + +function install_uclust() { + install_R-4.3.0 + cd $install_path + R -e 'install.packages("uclust")' +} + + +function install_onemap() { + install_R-4.3.0 + cd $install_path + R -e 'install.packages("onemap", dependencies=TRUE)' +} + + +function install_poppr() { + install_R-4.3.0 + cd $install_path + R -e 'install.packages("poppr")' +} + + + +function install_seurat-5.0.0() { + install_R-4.3.0 + cd $install_path + wget https://github.com/satijalab/seurat/archive/refs/tags/v5.0.0.tar.gz + tar xvf v5.0.0.tar.gz + cd seurat-5.0.0/ + R -e 'install.packages("BiocManager")' + R -e 'BiocManager::install(c("SeuratObject", "cowplot", "fastDummies", "fitdistrplus", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "httr", "ica", "igraph", "irlba", "leiden", "lmtest", "matrixStats", "miniUI", "patchwork", "pbapply", "plotly", "png", "progressr", "RANN", "RColorBrewer", "RcppAnnoy", "RcppHNSW", "reticulate", "ROCR", "RSpectra", "Rtsne", "scales", "scattermore", "sctransform", "shiny", "spatstat.explore", "spatstat.geom", "tibble", "uwot", "RcppEigen", "RcppProgress"))' + R CMD INSTALL . +} + + +function install_reditools-2.0() { + cd $install_path + yum install environment-modules openmpi-devel -y + source /etc/profile + module load mpi/openmpi-aarch64 + git clone https://github.com/tizianoflati/reditools2.0 + cd reditools2.0 + pip3 install -r requirements.txt +} + +#װopenblas +function install_openblas() { + cd $install_path + wget https://github.com/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz + tar -xvf OpenBLAS-0.3.23.tar.gz + cd OpenBLAS-0.3.23 + make -j 16 ARCH=aarch64 all + make PREFIX=$targetdir/openblas/openblas_install install + echo export PATH=$targetdir/openblas/openblas_install/bin:\$PATH >> $source_file + echo export LD_LIBRARY_PATH=$targetdir/openblas/openblas_install/lib:\$LD_LIBRARY_PATH >> $source_file +} + +#װgsl +function install_gsl() { + cd $install_path + wget https://ftpmirror.gnu.org/gsl/gsl-2.7.1.tar.gz + tar -xf gsl-2.7.1.tar.gz + cd gsl-2.7.1/ + ./configure --prefix=$targetdir/gsl/gsl_install + make -j 16 + make install + echo export PATH=$targetdir/gsl/gsl_install/bin:\$PATH >> $source_file + echo export LD_LIBRARY_PATH=$targetdir/gsl/gsl_install/lib:\$LD_LIBRARY_PATH >> $source_file +} + +#װadmixtools +function install_admixtools() { + #װopenblas + install_openblas + #װgsl + install_gsl + cd $install_path + wget https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz + tar -xf v7.0.2.tar.gz + cd AdmixTools-7.0.2/src + sed -i '14d' Makefile + sed -i '18d' Makefile + sed -i "14s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile + sed -i "15s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile + make -j 16 + make install + mkdir -p $targetdir/admixtools/admixtools_install + cp -r ../bin $targetdir/admixtools/admixtools_install/bin + echo export PATH=$targetdir/admixtools/admixtools_install/bin:\$PATH >> $source_file +} + +#װEIG +function install_EIG() { + #װopenblas + install_openblas + #װgsl + install_gsl + cd $install_path + wget https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz + mv v8.0.0.tar.gz EIG-8.0.0.tar.gz + tar -xf EIG-8.0.0.tar.gz + cd EIG-8.0.0/src + sed -i "1s%^.*$%override CFLAGS += -I../include -I$targetdir/openblas/openblas_install/include%g" Makefile + sed -i '10d' Makefile + sed -i '12d' Makefile + sed -i "10s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile + sed -i "11s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile + make -j 16 + make install + mkdir -p $targetdir/EIG/EIG_install + cp -r ../bin $targetdir/EIG/EIG_install + cp -r ../include $targetdir/EIG_install + echo export PATH=$targetdir/EIG_install/bin:\$PATH >> $source_file +} + +#װgdal +function install_gadl() { + cd $install_path + yum install proj proj-devel -y + wget https://download.osgeo.org/gdal/3.7.0/gdal-3.7.0.tar.xz + tar -xf gdal-3.7.0.tar.xz + cd gdal-3.7.0/ + mkdir build + cd build + cmake ../ -DCMAKE_INSTALL_PREFIX=$targetdir/gdal/gdal_install + make install + echo export PATH=$targetdir/gdal/gdal_install/bin:\$PATH >> $source_file + echo export LD_LIBRARY_PATH=$targetdir/gdal/gdal_install/lib:\$LD_LIBRARY_PATH >> $source_file +} + +#װcommot +function install_commot() { + #װ + yum install python3-devel python3 python3-pip git make -y + install_gadl + source $source_file + pip install commot -i https://pypi.tuna.tsinghua.edu.cn/simple +} + +function install_asset() { +# װ + pip3 install asset +} + + +function install_astral() { + #װ + cd $install_path + wget https://github.com/smirarab/ASTRAL/archive/refs/tags/v5.7.1.tar.gz -O ASTRAL-5.7.1.tar.gz + tar -zxf ASTRAL-5.7.1.tar.gz + cd ASTRAL-5.7.1 + sh make.sh + echo "PATH=$inspath/ASTRAL-5.7.1:$PATH" >> $source_file +} + + +function install_bayescan() { + #װ + cd $install_path + wget https://github.com/mfoll/BayeScan/archive/refs/tags/v2.1.tar.gz + tar xvf v2.1.tar.gz + cd BayeScan-2.1/ + make -j + echo "PATH=$inspath/BayeScan-2.1:$PATH" >> $source_file +} + +function install_daligner() { + #װ + cd $install_path + wget https://github.com/thegenemyers/DALIGNER/archive/refs/tags/V1.0.tar.gz -O DALIGNER-1.0.tar.gz + tar -zxf DALIGNER-1.0.tar.gz + cd DALIGNER-1.0/ + make -j + echo "PATH=$inspath/DALIGNER-1.0:$PATH" >> $source_file +} + +function install_ectools() { + #װ + cd $install_path + wget https://github.com/jgurtowski/ectools/archive/refs/tags/v0.1.tar.gz -O ectools-0.1.tar.gz + tar -xvf ectools-0.1.tar.gz + cd ectools-0.1/ + cd test + ../schtats -log -stdout test.sim.fa +} + + +function install_EVidenceModeler() { + #װ + cd $install_path + yum install -y perl perl-URI + git clone --recursive https://github.com/EVidenceModeler/EVidenceModeler.git + cd EVidenceModeler + git checkout EVidenceModeler-v2.1.0 + sed -i "s/-m64//g" `grep -rl "\-m64"` + make -j + cd testing + ./runMe.sh +} + + +function install_FASconCAT() { + #װ + cd $install_path + git clone https://github.com/PatrickKueck/FASconCAT.git + cd FASconCAT/ + echo "PATH=$inspath/FASconCAT:$PATH" >> $source_file +} + +function install_GMcloser() { + #װ + cd $install_path + wget https://sourceforge.net/projects/gmcloser/files/GMcloser-1.6.2.tar.gz + tar xvf GMcloser-1.6.2.tar.gz + cd GMcloser-1.6.2 + ./gmcloser -h +} + +function install_3d-dna() { + #װ + cd $install_path + git clone https://github.com/theaidenlab/juicer.git + cd juicer + ln -s CPU scripts + cd scripts/common + wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar + ln -s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar + cd $install_path + git clone https://github.com/theaidenlab/3d-dna.git + ./juicer/scripts/juicer.sh -h + ./3d-dna/run-asm-pipeline.sh -h +} + + + +function install_allhic() { + install_go + mkdir -p $install_path/allhic + cd $install_path/allhic + mkdir src pkg bin + export GOPATH=$install_path/allhic + go env -w GO111MODULE=on + go env -w GOPROXY=https://goproxy.cn,direct + + wget https://github.com/tanghaibao/allhic/archive/refs/tags/v0.9.13.tar.gz + tar -xf v0.9.13.tar.gz + cd $install_path/allhic/allhic-0.9.13 + go mod init allhic + go mod tidy + cd $install_path/allhic/allhic-0.9.13/cmd + go install main.go + mv $install_path/allhic/bin/main $install_path/allhic/bin/allhic + yum install environment-modules -y + source /etc/profile + cat > $install_path/allhic/allhic_modulefiles << EOF +#%Module1.0 +conflict go +variable modfile [file normalize [info script]] +proc getModulefileDir {} { + variable modfile + set modfile_path [file dirname $modfile] + return $modfile_path +} +set pwd [getModulefileDir] +set allhic $pwd +setenv allhic $allhic +prepend-path PATH $allhic/bin +EOF + + echo module use $install_path/allhic >> $source_file + echo module use $install_path/allhic/allhic_modulefiles >> $source_file + source $source_file + allhic --version + + +} + + + +function install_yass() { + cd $install_path + wget https://codeload.github.com/laurentnoe/yass/tar.gz/refs/tags/1.16_alpha1 -O yass-1.16_alpha1.tar.gz + tar -xvf yass-1.16_alpha1.tar.gz + cd yass-1.16_alpha1/ + autoreconf + ./configure --with-threads --build=aarch64-unknown-linux-gnu + automake + make + cd src + ./yass -v +} + + +function install_amas() { + cd $install_path + #װ + wget https://codeload.github.com/marekborowiec/AMAS/zip/refs/heads/master -O AMAS.zip + unzip AMAS.zip + mv AMAS-master AMAS + cd AMAS + pip install virtualenv + virtualenv AMAS + source AMAS/bin/activate + cd $install_path/AMAS/ + ls + python3 setup.py install +} + + +function install_htslib() { + cd $install_path + wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 + tar -xvf htslib-1.16.tar.bz2 + cd htslib-1.16 + yum -y install zlib-devel bzip2-devel xz-devel + ./configure + make -j + make install +} + + +function install_angsd() { + cd $install_path + install_htslib + wget http://popgen.dk/software/download/angsd/angsd0.938.tar.gz + yum -y install curl curl-devel + make HTSSRC=/usr/local/lib +} + +function install_yak() { + cd $install_path + wget https://codeload.github.com/lh3/yak/tar.gz/refs/tags/v0.1 -O yak-0.1.tar.gz + tar -xvf yak-0.1.tar.gz + cd yak-0.1/ + make -j +} + + +function install_art-nextgen-simulation-tools() { + cd $install_path + yum -y install gsl gsl-devel + wget https://mirror.tuna.tsinghua.edu.cn/raspbian/raspbian/pool/main/a/art-nextgen-simulation-tools/art-nextgen-simulation-tools_20160605%2Bdfsg.orig.tar.xz + tar -xvf art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz + cd art_src_MountRainier_Linux + autoreconf --install + ./configure --prefix=$install_path/art-nextgen-simulation-tools-install + make -j + make install +} + +function install_idba() { + cd $install_path + wget https://codeload.github.com/abishara/idba/tar.gz/refs/tags/1.1.3a1 -O idba-1.1.3a1.tar.gz + tar -xvf idba-1.1.3a1.tar.gz + cd idba-1.1.3a1/ + ./build.sh +} + + +#samtools +function install_samtools() { + #gcc-10.3.1 + cd $install_path + wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O samtools-0.1.9.tar.gz + tar -xvf samtools-0.1.9.tar.gz + cd samtools-0.1.9 + make + echo export PATH=$install_path/samtools-0.1.9:\$PATH >> $source_file +} + + +function install_samtools-1.16.1() { + cd $install_path + wget https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2 + tar -xvf samtools-1.16.1.tar.bz2 + cd samtools-1.16.1 + make -j && make install +} + +function install_minimap2() { + git clone https://github.com/lh3/minimap2.git + cd minimap2/ + make arm_neno=1 aarch64=1 +} + + +function install_flye() { #bug + cd $install_path + install_gcc + git clone https://github.com/fenderglass/Flye.git + cd Flye/ + git checkout 2.3.1 + cd ./lib/minimap2 + wget https://raw.githubusercontent.com/DLTcollab/sse2neon/master/sse2neon.h + cd - + sed -i 's//\"sse2neon.h\"/g' ./lib/minimap2/ksw2_ll_sse.c + python setup.py install +} + +function install_szip() { + cd $install_path + wget https://distfiles.macports.org/szip/szip-2.1.1.tar.gz + tar xf szip-2.1.1.tar.gz + cd szip-2.1.1/ + ./configure --prefix=$install_path/sizp + make && make install +} + +function install_hdf5() { + cd $install_path + wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz + tar xf hdf5-1.8.12.tar.gz + cd hdf5-1.8.12 + ./configure --enable-cxx --enable-static=yes --enable-shared --prefix=$install_path/hdf5/hdf5-1.8.12 --build=arm LDFLAGS="-L$install_path/szip/szip-2.1.1/lib" CPPFLAGS="-I$install_path/szip/szip-2.1.1/include" + make -j + make install +} + + +function install_blasr() { + wget https://codeload.github.com/BioinformaticsArchive/blasr/zip/refs/heads/master -O blasr-master.zip + unzip blasr-master.zip + cd blasr-master/ + sed -i "5c\HDF5INCLUDEDIR=$install_path/hdf5/hdf5-1.8.12/include" common.mk + sed -i "6c\HDF5LIBDIR=$install_path/hdf5/hdf5-1.8.12/lib" common.mk + sed -i "s/\-static//g" `grep -rnl "\-static"` + sed -i "13s/$/ -ldl/" common.mk + sed -i "33s/testIn/testIn.good()/g" ./common/data/hdf/HDFFile.h + sed -i "242c\ (unsigned int) curPrefix.tuple + 1 < (unsigned int) (this->lookupTableLength));" ./common/datastructures/suffixarray/SuffixArray.h + sed -i "2271s/cout <> $source_file +} + +function install_ViennaRNA() { + cd $install_path + wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.4.tar.gz + tar -zxvf ViennaRNA-2.4.4.tar.gz + cd ViennaRNA-2.4.4/ + cd ViennaRNA-2.4.4 + ./configure --prefix=/path/to/ViennaRNA -build=arm-linux + make + make install +} + + + +function install_hifiasm() { + cd $install_path + git clone https://github.com/chhylp123/hifiasm.git + git clone https://github.com/DLTcollab/sse2neon.git + export C_INCLUDE_PATH=$install_path/sse2neon + export CPLUS_INCLUDE_PATH=$install_path/sse2neon + sed -i 's/#include /#include /g' ksw2_extz2_sse.c + sed -i 's/#include /#include /g' Levenshtein_distance.h + sed -i 's/#include \"smmintrin.h\"//g' Levenshtein_distance.h + sed -i 's/#include \"nmmintrin.h\"//g' Levenshtein_distance.h + sed -i 's/#include \"emmintrin.h\"//g' Levenshtein_distance.h + make +} + +yum -y install python3 python3-devel python3-pip +pip install virtualenv + + + + +function install_taxonkit() { + cd $install_path + install_go + git clone https://github.com/shenwei356/taxonkit + cd taxonkit/taxonkit/ + go build + echo export PATH=$install_path/taxonkit/taxonkit:\$PATH >> $source_file +} + + + + +function install_cdhit() { #bug + install_bisheng + wget https://github.com/weizhongli/cdhit/archive/refs/tags/V4.8.1.tar.gz + tar -xvf V4.8.1.tar.gz + cd cdhit-4.8.1 + sed -i "1,3s/g++/clang/g" Makefile + make +} + + +function install_raxml-ng() { + git clone --recursive https://github.com/amkozlov/raxml-ng.git + cd raxml-ng/ + mkdir build && cd build + cmake .. + make install +} + +function install_interval() { + cd $install_path + pip2 install docopt==0.6.2 + pip2 install pysam + git clone https://github.com/kepbod/interval.git + cd interval/ + python2 setup.py install + echo export PATH=$install_path/interval/build/lib:$PATH >> $source_file +} + + +function install_CIRCexplorer() { + cd $install_path + install_interval + wget https://github.com/YangLab/CIRCexplorer/archive/refs/tags/1.1.10.tar.gz + tar -xvf 1.1.10.tar.gz + cd CIRCexplorer-1.1.10/ + python2 setup.py install + CIRCexplorer.py -h +} + + + +function install_wise() { #bug + install_gcc + wget https://src.fedoraproject.org/repo/extras/wise2/wise2.4.1.tar.gz/d70c404c1dc40ceef7718757b11bdaa0/wise2.4.1.tar.gz + tar -xvf wise2.4.1.tar.gz + cd wise2.4.1 + cd src/ + find . -name makefile | xargs sed -i 's/glib-config/pkg-config glib-2.0/' + perl -p -i -e 's/getline/getline_ReadSeqVars/g' ./HMMer2/sqio.c + perl -p -i -e 's/isnumber/isdigit/' models/phasemodel.c + perl -p -i -e's/csh welcome.csh/sh welcome.csh/' makefile + sed -i 's/-ldyna_glib/-ldyna_glib `pkg-config --libs glib-2.0`/' models/makefile + make all +} + + +function install_beast() { + cd $install_path + wget https://github.com/CompEvol/beast2/releases/download/v2.7.0/BEAST.v2.7.0.Linux.aarch64.tgz + tar xvf BEAST.v2.7.0.Linux.aarch64.tgz + yum -y install java-devel + echo export PATH=$install_path/beast/bin/:$PATH >> $source_file +} + + + +function install_bioperl() { + pip2 install numpy + pip2 install biopython==1.76 + wget -O - https://install.perlbrew.pl | bash + cd /root/perl5/perlbrew/bin/ + ./perlbrew install-cpanm + ./cpanm install Bio::Perl +} + +function install_CPC() { + cd $install_path + install_bioperl + wget http://cpc2.gao-lab.org/data/CPC2-beta.tar.gz + tar -xf CPC2-beta.tar.gz + cd CPC2-beta/ + export CPC_HOME=`pwd` + cd libs/libsvm/ + tar -xf libsvm-3.18.tar.gz + cd libsvm-3.18/ + make + sed -i -e "s/print \(.*\)/print \(\1\)/g" ./bin/seqio.py + sed -i "s/ file(/ open(/g" ./bin/CPC2.py + python2 bin/CPC2.py +} + +function install_hpcrunner() { + cd $install_path + git clone https://gitee.com/sunlock0653/hpcrunner.git +} + +function install_CMAQ() { + install_hpcrunner + cd $install_path/hpcrunner + git checkout EA-1.0 + source ./init.sh + ./jarvis -use templates/CMAQ/5.3.1/data.CMAQ.arm_kgcc.cpu.config + ./jarvis -d + ./jarvis -dp + ./jarvis -b + + module use $install_path/hpcrunner/software/modulefiles + module purge + module load kgcc/9.3.1 + module load hmpi/1.1.1 + module load hdf5/1.10.1 + module load netcdf/4.7.0 + module load optimized-routines/20.02 + module load ioapi/3.2 +} + +function install_wavewatch() { + cd $install_path + git clone https://github.com/NOAA-EMC/WW3.git + ./model/bin/w3_setup model -c Gnu -s NCEP_st4 + export WWATCH3_NETCDF=NC4 + export NETCDF_CONFIG=`which nc-config` + + cd model/bin + ./w3_automake +} + + +function install_POM() { + install_CMAQ + module use $install_path/hpcrunner/software/modulefiles + module purge + module load kgcc/9.3.1 + module load hmpi/1.1.1 + module load hdf5/1.10.1 + module load netcdf/4.7.0 + module load optimized-routines/20.02 + module load ioapi-kgcc/3.2 + + cd $install_path + wget -r -p -k -np -nc -e robots=off http://www.ccpo.odu.edu/POMWEB/GRID-DATA + wget -r -p -k -np -nc -e robots=off http://www.ccpo.odu.edu/POMWEB/POM2K + cd $install_path/www.ccpo.odu.edu/POMWEB/POM2K + rm -rf runpom2k + wget https://gitee.com/sunlock0653/hpcrunner/raw/EA-1.0/wait_file/runpom2k + chmod 755 runpom2k + ./runpom2k +} + +function install_camx() { + wget https://www.camx.com/getmedia/CAMx_v7.20.src.220430.tgz + module use $install_path/hpcrunner/software/modulefiles + module purge + module load kgcc/9.3.1 + module load hmpi/1.1.1 + module load hdf5/1.10.1 + module load netcdf/4.7.0 + module load optimized-routines/20.02 + sed -i -e "s#\/usr\/local\/mpich3#${install_path}/hpcrunner\/software\/mpi\/hmpi1.1.1-kgcc9.3.1\/1.1.1#g" Makefile + cd ./MPI/util + sed -i -e "s#\/usr\/local\/mpich-3.0.4.pgi.2019.CE#${install_path}/hpcrunner\/software\/mpi\/hmpi1.1.1-kgcc9.3.1\/1.1.1#g" Makefile + cd - + make COMPILER=gfortran CONFIG=v7.20 MPI=mpich3 IEEE=true +} + + +function install_swan() { + install_cmake + git clone https://gitlab.tudelft.nl/citg/wavemodels/swan.git && cd swan + mkdir build && cd build + cmake .. -G Ninja + cmake --build . +} + +function install_mitgcm() { + cd $install_path + module use $install_path/hpcrunner/software/modulefiles + module purge + module load kgcc/9.3.1 + module load hmpi/1.1.1 + module load hdf5/1.10.1 + module load netcdf/4.7.0 + wget http://mitgcm.org/download/other_checkpoints/MITgcm_c67o.tar.gz + tar -xvf MITgcm_c67o.tar.gz + git clone https://gitee.com/kp-hpc-mod/hpc-patch.git + patch -p0 < hpc-patch/patch_file/MITgcm_c67o.patch + cd MITgcm + cd verification/exp4/build + ../../../tools/genmake2 -mods=../code -mpi -of=../../../tools/build_options/linux_arm64_gfortran + make depend + make -j +} + + +function create_virtualenv(){ + cd $install_path + pip3 install virtualenv -i https://pypi.tuna.tsinghua.edu.cn/simple + yum install python3 python3-devel python3-pip + python3 -m virtualenv $install_path + #pip2 install virtualenv -i https://pypi.tuna.tsinghua.edu.cn/simple + #yum install python2 python2-devel python2-pip + #python -m virtualenv $install_path + source $install_path/bin/activate +} + +function install_cpat() { + pip3 install cpat +} + +function install_CIRI() { + wget https://sourceforge.net/projects/ciri/files/CIRI2/CIRI_v2.0.6.zip + unzip CIRI_v2.0.6.zip + cd CIRI_v2.0.6/ +} + + +function install_trimmomatic() { + wget https://github.com/timflutre/trimmomatic/archive/refs/heads/master.zip + unzip master.zip.2 + cd trimmomatic-master/ + make -j + make install INSTALL=/path/to/trimmomatic-install + +} + + +function install_spliceGrapher() { + cd $install_path + wget https://master.dl.sourceforge.net/project/splicegrapher/SpliceGrapher-0.2.7.tgz + tar -xvf SpliceGrapher-0.2.7.tgz + rm -rf SpliceGrapher-0.2.7.tgz + git clone https://gitee.com/kp-hpc-mod/hpc-patch.git + patch -p0 < hpc-patch/patch_file/SpliceGrapher-0.2.7.patch + tar -zcvf SpliceGrapher-0.2.7.tgz SpliceGrapher-0.2.7 + pip3 install SpliceGrapher-0.2.7.tgz + #pip2 install SpliceGrapher-0.2.7.tgz +} + + +function install_svmu() { + wget https://codeload.github.com/mahulchak/svmu/tar.gz/refs/tags/0.3-alpha -O svmu-0.3-alpha.tar.gz + tar -xvf svmu-0.3-alpha.tar.gz + cd svmu-0.3-alpha/ + make +} + +function install_MrBayes() { + cd $install_path + wget https://codeload.github.com/NBISweden/MrBayes/tar.gz/refs/tags/v3.2.7 -O MrBayes-3.2.7.tar.gz + tar -xvf MrBayes-3.2.7.tar.gz + cd MrBayes-3.2.7/ + ./configure + make && sudo make install +} + +function install_tapis() { + create_virtualenv + install_spliceGrapher + pip3 install numpy bx-python pysam matplotlib streams -i https://pypi.tuna.tsinghua.edu.cn/simple + pip3 install django-activity-stream -i https://pypi.tuna.tsinghua.edu.cn/simple + cd $install_path + git clone https://bitbucket.org/singhbit/tapis.git + cd $install_path/tapis + python3 setup.py build + pip3 install . +} + + + +conda create -n envname python=3.8 +conda activate envname +pip3 install numpy -i https://pypi.tuna.tsinghua.edu.cn/simple +pip3 install cython -i https://pypi.tuna.tsinghua.edu.cn/simple +pip3 install mdtraj -i https://pypi.tuna.tsinghua.edu.cn/simple +pip3 install pandas>=1.4 -i https://pypi.tuna.tsinghua.edu.cn/simple +cd $install_path +git clone https://github.com/LQCT/MDScan.git +cd MDScan/ +pip3 install . -i https://pypi.tuna.tsinghua.edu.cn/simple + + + + +function install_htslib() { + yum install zlib-devel bzip2 bzip2-devel xz-devel -y + cd $install_path + wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2 + tar -jxvf htslib-1.10.2.tar.bz2 + cd htslib-1.10.2/ + ./configure --prefix=cd $install_path/htslib + make -j + make install + ln -s /usr/local/lib/libhts.so.3 /usr/lib/libhts.so.3 + sudo ldconfig +} + +function install_pindel() { + install_htslib + cd $install_path + git clone https://github.com/genome/pindel.git + cd pindel/ + ./INSTALL ../htslib-1.10.2 + ./INSTALL ../htslib-1.10.2 + ./bam2pindel.pl + +} + + + +function install_szip() { + cd $install_path + wget https://distfiles.macports.org/szip/szip-2.1.1.tar.gz + tar xf szip-2.1.1.tar.gz + cd szip-2.1.1 + ./configure --prefix=/path/to/szip + make + make install +} + +function install_networkx() { + wget https://pypi.tuna.tsinghua.edu.cn/packages/f1/8e/f6f345ed7b228d080e338eac5a6bcce2260390468ae9130dcb67096f59c4/networkx-1.1.tar.gz + tar -xvf networkx-1.1.tar.gz + cd networkx-1.1 + python setpu.py install +} + +function install_pysam() { + wget https://pypi.tuna.tsinghua.edu.cn/packages/a4/ea/901d47d5621f15c05079dcf45e746a77bab21dbf0f9ce272993a3ca3a367/pysam-0.8.0.tar.gz + tar -xvf pysam-0.8.0.tar.gz + cd pysam-0.8.0/ + python setup.py install +} + + + + + +function install_blasr() { + pip install intervaltree==2.1.0 -i https://pypi.tuna.tsinghua.edu.cn/simple + pip install intervaltree-bio==1.0.1 -i https://pypi.tuna.tsinghua.edu.cn/simple + install_networkx + pip install numpy==1.16.6 -i https://pypi.tuna.tsinghua.edu.cn/simple + pip install PyIntervalTree==0.5 -i https://pypi.tuna.tsinghua.edu.cn/simple + install_pysam + pip install PyVCF==0.6.8 -i https://pypi.tuna.tsinghua.edu.cn/simple + install_hdf5 + cd $install_path + git clone https://github.com/HWsunqian0027/blasr.git + export HDF5INCLUDEDIR= $install_path/hdf5/hdf5-1.8.12/include + export HDF5LIBDIR= $install_path/hdf5/hdf5-1.8.12/lib/ + cd blasr/ + make +} + + +function install_PBSuite() { + wget https://sourceforge.net/projects/pb-jelly/files/PBSuite_15.8.24.tgz + tar -xvf PBSuite_15.8.24.tgz + cd PBSuite_15.8.24/ + a=`pwd` + sed -i "s#SWEETPATH=.*#SWEETPATH=$a#g" setup.sh + source ./setup.sh + ./bin/Jelly.py --help +} + + + + + +function install_clustalw() { + wget http://www.clustal.org/download/current/clustalw-2.1.tar.gz + tar -xvf clustalw-2.1.tar.gz + mv config.guess config.guess_bak + mv config.sub config.sub_bak + cp /usr/share/automake-1.16/config.* . + ./configure + make +} + + + + + + + +function install_hycom() { +cd $install_path +wget https://github.com/HYCOM/HYCOM-src/releases/download/2.3.01/HYCOM-src_2.3.01.tar.gz +chsh -s /bin/csh +module use $install_path/hpcrunner/software/modulefiles +module purge +module load kgcc/9.3.1 +module load hmpi/1.1.1 +tar -xvf HYCOM-src_2.3.01.tar.gz +#wget https://gitee.com/-/ide/project/kp-hpc-mod/hpc-patch/edit/master/-/patch_file/HYCOM-src_2.3.01.patch +git clone https://gitee.com/kp-hpc-mod/hpc-patch.git +patch -p0 < hpc-patch/patch_file/HYCOM-src_2.3.01.patch +cd HYCOM-src_2.3.01/ +./Make.csh +chsh -s /bin/bash +} + + + + +#------exagear--------------------# +if [ "$1" == "bayenv2_public" ];then + git clone https://bitbucket.org/tguenther/bayenv2_public.git + ./bayenv2 -i hgdp_no_X_37_freqs -e PCs.env -m hgdp_matrix_1 -s samplesize.txt -k 10 -p 10 +fi + + +wget https://github.com/CEMPD/SMOKE/archive/refs/tags/SMOKEv5_Jun2023.tar.gz +tar -xvf SMOKEv5_Jun2023.tar.gz +cd SMOKE-SMOKEv5_Jun2023/scripts/install +chmod +x smoke_install_v47.csh +./smoke_install_v47.csh + + + if [ ! -n "$OPT" ]; then install_$OPT + else source $source_file fi \ No newline at end of file diff --git a/package/octopus/11.4/install.sh b/package/octopus/11.4/install.sh new file mode 100644 index 0000000..a494c9d --- /dev/null +++ b/package/octopus/11.4/install.sh @@ -0,0 +1,155 @@ +#!/bin/bash + +##ȫֱ +#--------------------------------# +#having test +version=$1; + +##ȫֱ +#--------------------------------# +passwd=123456; +install_path=/share/home/top_software/sunqian +target_path=$install_path/bin +source_file=$install_path/source_sun.sh +cpu_num=`grep -c "processor" /proc/cpuinfo`; #CPU +netcard=`cat /proc/net/dev|sort -rn -k2|awk '{print $1}'|awk NR==1|awk -F ':' '{print $1}'`;# +ip_addr=`ip a|grep $netcard|grep inet|awk '{print $2}'|awk -F '/' '{print $1}'` #ipַ +osType=`cat /etc/os-release|grep ID |awk NR==1|awk -F \" '{print $2}'` +basearch=`arch` +#--------------------------------# +echo install_path=/share/home/top_software/sunqian >> $source_file +touch $source_file +#--------------------------------# +#ȫ +cd $install_path +wget https://ftp.gnu.org/gnu/gsl/gsl-2.5.tar.gz +wget https://launchpad.net/libvdwxc/stable/0.4.0/+download/libvdwxc-0.4.0.tar.gz +wget https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.10.1.tar.gz +wget http://forge.abinit.org/fallbacks/libxc-4.0.1.tar.gz +wget http://www.fftw.org/fftw-3.3.8.tar.gz +wget https://octopus-code.org/download/11.4/octopus-11.4.tar.gz +wget https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.2.0-huawei.tar.gz + + + + +#װlibxc 4.0.1 +cd $install_path +tar -xvf libxc-4.0.1.tar.gz +cd libxc-4.0.1 +CC=gcc +FC="gfortran -fallow-argument-mismatch" +./configure --prefix=$target_path/libxc --enable-shared=yes --enable-static=yes +make -j$(nproc) +make install + + +cat>"$target_path/libxc/libxc_modulefiles"<"$target_path/octopus/octopus-11.4/octopus_modulefiles"< Date: Fri, 6 Dec 2024 16:33:11 +0800 Subject: [PATCH 7/7] fix wrf --- package/lifescience/install.sh | 2030 ----------------- .../wrf/4.3.3/bisheng/data.wrf.arm.cpu.config | 83 +- 2 files changed, 66 insertions(+), 2047 deletions(-) delete mode 100644 package/lifescience/install.sh diff --git a/package/lifescience/install.sh b/package/lifescience/install.sh deleted file mode 100644 index b045a80..0000000 --- a/package/lifescience/install.sh +++ /dev/null @@ -1,2030 +0,0 @@ -#!/bin/bash - -#ѧ װʹܽűҪװrandfoldִ -# sh hpc_life_science.sh randfold -#ʹӦִ -#sh hpc_life_science.sh - -#--------------------------------# -OPT=$1; - -##ȫֱ -#--------------------------------# -passwd=123456; -install_path=/home/hpc_software/ -targetdir=$install_path/BIN -source_file=$install_path/source.sh -cpu_num=`grep -c "processor" /proc/cpuinfo`; #CPU -netcard=`cat /proc/net/dev|sort -rn -k2|awk '{print $1}'|awk NR==1|awk -F ':' '{print $1}'`;# -ip_addr=`ip a|grep $netcard|grep inet|awk '{print $2}'|awk -F '/' '{print $1}'` #ipַ -osType=`cat /etc/os-release|grep ID |awk NR==1|awk -F \" '{print $2}'` -basearch=`arch` - - - -#--------------------------------# -mkdir -p $targetdir -echo install_path=$install_path >> $source_file -touch $source_file - - -#--------------------------------# -#ȫ -cd $install_path -yum -y install make gcc g++ git -yum install -y java-1.8.0-openjdk-devel.aarch64 ncurses-devel.aarch64 bzip2-devel.aarch64 python3-devel python bazel -pip3 install tensorflow - -#GSEA -function install_GSEA() { -#װjava -yum install java-11-openjdk-devel.aarch64 -y -#װӻ -#yum install xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -y -#sed -i "s/X11Forwarding no/X11Forwarding yes/g" /etc/ssh/sshd_config -#systemctl restart sshd.service -cd $install_path -wget https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip -unzip GSEA_4.3.2.zip -echo export PATH=$install_path/GSEA_4.3.2:\$PATH >> $source_file -} - -#pangolin -function install_pangolin() { -#װ -yum install python3-devel python3 python3-pip git make -y -cd $install_path -wget https://github.com/cov-lineages/pangolin/archive/refs/tags/v4.3.1.tar.gz -O pangolin-v4.3.1.tar.gz -tar xf pangolin-v4.3.1.tar.gz -cd pangolin-4.3.1 -pip3 install . -i https://pypi.tuna.tsinghua.edu.cn/simple -pip3 install git+https://github.com/cov-lineages/pangolin-data.git -pip3 install git+https://github.com/cov-lineages/scorpio.git -pip3 install git+https://github.com/cov-lineages/constellations.git -pip3 install snakemake -i https://pypi.tuna.tsinghua.edu.cn/simple -} - - - -#randfold -function install_randfold() { -cd $install_path -git clone https://github.com/eb00/randfold.git -cd randfold/src/squid-1.9g -./configure && make -cd ../ -make -echo export PATH=$install_path/randfold/src >> $source_file -} - - - - - - - -#Rosetta -function install_Rosetta() { -yum -y install openssl-devel -pip3 install tensorflow nltk pandas -pip3 install tensorflow Rosetta -} - -#AlphaFold -function install_AlphaFold() { -pip3 install AlphaFold -} - -#STAR -function install_gatk() { -cd $install_path -wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.1a.tar.gz -O STAR-2.7.1a.tar.gz -tar -xvf STAR-2.7.1a.tar.gz && cd STAR-2.7.1a -sed -i 's/\?\=/\?= \-flto \-march=native \-mcpu=tsv110/g' source/Makefile|grep ? -cd source -make STAR -echo export PATH=$install_path/STAR-2.7.1a/source/:\$PATH >> $source_file -} - - -#ncbi-vdb -function install_ncbi-vdb() { -cd $install_path -wget https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.0.tar.gz -O ncbi-vdb-3.0.0.tar.gz -yum -y install doxygen cmake -yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y -tar -xvf ncbi-vdb-3.0.0.tar.gz -cd ncbi-vdb-3.0.0 -cp -r interfaces/cc/gcc/arm64 interfaces/cc/gcc/aarch64 -./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 --prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 -make -j $(nproc) && make install -} - - -#sratoolkit-3.0.0 -function install_sratoolkit() { -install_ncbi-vdb -cd $install_path -wget https://github.com/ncbi/sra-tools/archive/refs/tags/3.0.0.tar.gz -O sratoolkit-3.0.0.tar.gz -yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y -tar zxvf sratoolkit-3.0.0.tar.gz -cd sra-tools-3.0.0 -cd tools/sharq/bm/ -wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/bmutil.h.patch - -patch -p0 < bmutil.h.patch -cd ../../../ -cd tools/copycat/ -wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/ccsra.c.patch -patch -p0 < ccsra.c.patch -cd ../../ -sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" tools/sharq/CMakeLists.txt -sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" test/sharq/CMakeLists.txt -cd tools/driver-tool/secure/ -wget https://gitee.com/openeuler/AvxToNeon/blob/master/avx2neon.h -sed -i 's/#include /#include /' string.cpp -cd ../../../ -./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --with-ncbi-vdb-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 -make -j $(nproc) -make install - -echo export $targetdir/sratoolkit/sra-tools-3.0.0/bin >> $source_file - -} - - -#cutadapt -function install_cutadapt() { -pip3 install cutadapt==4.1 -#pip3 install cutadapt -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com -} - - - -#Bowtie2 -function install_Bowtie2() { -cd $install_path -wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.4.1.tar.gz -O bowtie2-2.4.1.tar.gz -yum install zlib.aarch64 zlib-devel.aarch64 zlib-static.aarch64 -tar -xvf bowtie2-2.4.1.tar.gz -cd bowtie2-2.4.1 -mkdir -p third_party/simde/simde/x86/ -export NO_TBB=1 -export POPCNT_CAPABILITY=0 -wget https://codeload.github.com/simd-everywhere/simde/tar.gz/refs/tags/v0.7.6 -O simde-0.7.6.tar.gz -tar -xvf simde-0.7.6.tar.gz - -wget https://codeload.github.com/jratcliff63367/sse2neon/zip/refs/heads/master -O sse2neon.zip - -cp -a simde-0.7.6/simde third_party/simde/ -cp sse2neon-master/SSE2NEON.h sse2neon-master/sse2neon.h -cp -a sse2neon-master/sse2neon.h ./third_party/simde/simde/x86/ -make all -echo export PATH=$install_path/bowtie2-2.4.1:\$PATH >> $source_file -} - - - -#deeptool -function install_deeptool() { -cd $install_path -wget https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz -O deepTools-3.5.1.tar.gz -tar -xvf deepTools-3.5.1.tar.gz -cd $install_path/deepTools-3.5.1 -python3 setup.py install -} - - - -#meme -function install_meme() { -cd $install_path -wget https://meme-suite.org/meme/meme-software/5.4.0/meme-5.4.0.tar.gz -tar -xvf meme-5.4.0.tar.gz -cd meme-5.4.0 -yum install -y libtool* autoconf automake nodejs* perl* libxml2* libxslt* -#cpan XML::Simple -#cpan Sys::info -#cpan Math::CDF -#cpan HTML::TreeBuilder.pm -#cpan JSON -./configure --prefix=$targetdir/MEME -make -make install -echo export PATH=$targetdir/MEME/bin:\$PATH >> $source_file -} - - -#ncbi-blast -function install_ncbi-blast() { -cd $install_path -wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-src.tar.gz -O ncbi-blast-2.13.0+-src.tar.gz -tar xzf ncbi-blast-2.13.0+-src.tar.gz -cd ncbi-blast-2.13.0+-src -export BLAST_TOP=`pwd` -export CC=gcc -export CXX=g++ -cd $BLAST_TOP -tar -xvf LMDB_0.9.24.tar.gz -cd lmdb-LMDB_0.9.24 -export LMDB_PATH=$BLAST_TOP/lmdb-LMDB_0.9.24 -cd $BLAST_TOP/c++ -./configure -cd ReleaseMT/build -make all_r -j -make -j && make install -cd $BLAST_TOP/c++/ReleaseMT/bin -ls blastp -blastp -} - -#emboss -function install_emboss() { -cd $install_path -wget ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz -yum install -y epel-release -yum install -y gcc -yum install -y gcc-c++ -yum install -y cmake -yum install -y make -yum install -y libX11 -yum install -y libX11-devel -tar -zxvf EMBOSS-6.5.7.tar.gz -cd EMBOSS-6.5.7/ -./configure --prefix=$targetdir/EMBOSS --build=aarch64-unknown-linux-gnu -make -j -make install -cd $targetdir/EMBOSS/bin -echo export PATH=$targetdir/EMBOSS/bin:\$PATH >> $source_file -} - -# -function install_TRF() { -cd $install_path -#git clone https://github.com/Benson-Genomics-Lab/TRF.git -wget https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz -O TRF-4.09.1.tar.gz -tar -xvf TRF-4.09.1.tar.gz -cd TRF-4.09.1 -mkdir build -cd build -../configure --prefix=$targetdir/RepeatMasker/TRF_install -make -j -make install -} - -#ncbi-blast-2.10.0 -function install_ncbi-blast-2.10.0() { -cd $install_path -wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz -wget https://www.repeatmasker.org/rmblast/isb-2.10.0+-rmblast.patch.gz -tar -xvf ncbi-blast-2.10.0+-src.tar.gz -gunzip isb-2.10.0+-rmblast.patch.gz -cd ncbi-blast-2.10.0+-src -patch -p1 < ../isb-2.10.0+-rmblast.patch -cd c++ -wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/B_patch.cpp -patch $install_path/ncbi-blast-2.10.0+-src/c++/src/build-system/configure ./B_patch.cpp -./configure --with-mt --without-debug --without-krb5 --without-openssl --with-projects=scripts/projects/rmblastn/project.lst --prefix=$targetdir/rmblast/rmblast_install -make -j && make -make install -} - -#repeatmaster -function install_repeatmaster() { -install_TRF -install_ncbi-blast-2.10.0 - -yum install perl perl-CPAN -y -cd $install_path -wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz -tar -xvf RepeatMasker-4.1.2-p1.tar.gz -cd RepeatMasker -yum install python3 python3-pip pip3 install h5py -chmod -R 755 * -./configure - -#²$targetdirҪ滻ɱֵ -#$targetdir/RepeatMasker/TRF_install/bin/trf -# 2 -#$targetdir/rmblast/rmblast_install/bin/ -# y -#5 -echo export PATH=$install_path/RepeatMasker:\$PATH >> $source_file -} - - - -function install_bats-0.4.0() { -cd $install_path -wget https://github.com/sstephenson/bats/archive/refs/tags/v0.4.0.tar.gz -tar -xvf v0.4.0.tar.gz -cd bats-0.4.0 -echo export PATH=$install_path/bats-0.4.0/bin:\$PATH >> $source_file -} - -function install_pygtftk-1.6.2() { -install_bats-0.4.0 -cd $install_path -wget https://github.com/dputhier/pygtftk/archive/refs/tags/v1.6.2.tar.gz -tar xvf v1.6.2.tar.gz -cd pygtftk-1.6.2 -pip3 install -r requirements.txt -pip3 install cython==0.29.30 -python3 setup.py install -} - - -function install_python-3.11.5() { -cd $install_path -wget https://www.python.org/ftp/python/3.11.5/Python-3.11.5.tar.xz -tar xvf Python-3.11.5.tar.xz -cd Python-3.11.5 -./configure --prefix=$targetdir/python_3_11_5/python_3_11_5_install -make -j -make install -echo export PATH=$targetdir/python_3_11_5/python_3_11_5_install/bin:\$PATH >> $source_file -echo export LD_LIBRARY_PATH=$targetdir/python_3_11_5/python_3_11_5_install/lib:$LD_LIBRARY_PATH >> $source_file -echo export INCLUDE=/$targetdir/python_3_11_5/python_3_11_5_install/include:$INCLUDE >> $source_file -} - - -function install_snakemake-7.32.4() { -install_python-3.11.5 -install_BWA -install_samtools -cd $install_path -wget https://files.pythonhosted.org/packages/f4/94/884160dab89886cef7802df0a8c8217bfb2d795427dee01ad0e0dc15964a/snakemake-7.32.4.tar.gz -tar xvf v7.32.4.tar.gz -cd snakemake-7.32.4 -pip3 install . -} - -function install_lapack-3.8.0() { -cd $install_path -wget https://www.cp2k.org/static/downloads/lapack-3.8.0.tgz -tar xvf lapack-3.8.0.tgz -cd lapack-3.8.0 -cp make.inc.example make.inc -sed -i "23s/$/ -fallow-argument-mismatch/g" make.inc -sed -i "25s/$/ -fallow-argument-mismatch/g" make.inc -mkdir build -cd build -cmake .. -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$targetdir/lapack_3_8_0/lapack_3_8_0_install -make -j -make install -echo export LD_LIBRARY_PATH=$targetdir/lapack_3_8_0/lapack_3_8_0_install/lib:$LD_LIBRARY_PATH >> $source_file -} - - -function install_scenic-1.3.1() { -install_R-4.3.0 -cd $install_path -R -e 'install.packages("BiocManager")' -R -e 'BiocManager::install("arrow")' -R -e 'install.packages("devtools")' -R -e 'devtools::install_github("aertslab/AUCell")' -R -e 'devtools::install_github("aertslab/RcisTarget")' -R -e 'devtools::install_github("aertslab/GENIE3")' -R -e 'BiocManager::install("ggrepel")' -R -e 'devtools::install_github("aertslab/SCENIC")' -} - -function install_seurat-5.0.0() { -install_R-4.3.0 -cd $install_path -wget https://github.com/satijalab/seurat/archive/refs/tags/v5.0.0.tar.gz -tar xvf v5.0.0.tar.gz -cd seurat-5.0.0/ -R -e 'install.packages("BiocManager")' -R -e 'BiocManager::install(c("SeuratObject", "cowplot", "fastDummies", "fitdistrplus", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "httr", "ica", "igraph", "irlba", "leiden", "lmtest", "matrixStats", "miniUI", "patchwork", "pbapply", "plotly", "png", "progressr", "RANN", "RColorBrewer", "RcppAnnoy", "RcppHNSW", "reticulate", "ROCR", "RSpectra", "Rtsne", "scales", "scattermore", "sctransform", "shiny", "spatstat.explore", "spatstat.geom", "tibble", "uwot", "RcppEigen", "RcppProgress"))' -R CMD INSTALL . -} - - -function install_reditools-2.0() { -cd $install_path -yum install environment-modules openmpi-devel -y -source /etc/profile -module load mpi/openmpi-aarch64 -git clone https://github.com/tizianoflati/reditools2.0 -cd reditools2.0 -pip3 install -r requirements.txt -} - - - -#װcommot -function install_commot() { -#װ -yum install python3-devel python3 python3-pip git make -y -install_gadl -source $source_file -pip install commot -i https://pypi.tuna.tsinghua.edu.cn/simple -} - - - -#!/bin/bash - -#ѧ װʹܽűҪװrandfoldִ -# sh hpc_life_science.sh randfold -#ʹӦִ -#sh hpc_life_science.sh - -#--------------------------------# -OPT=$1; - -##ȫֱ -#--------------------------------# -passwd=123456; -install_path=/home/sunqian -targetdir=$install_path/BIN -source_file=$install_path/source_sun.sh -cpu_num=`grep -c "processor" /proc/cpuinfo`; #CPU -netcard=`cat /proc/net/dev|sort -rn -k2|awk '{print $1}'|awk NR==1|awk -F ':' '{print $1}'`;# -ip_addr=`ip a|grep $netcard|grep inet|awk '{print $2}'|awk -F '/' '{print $1}'` #ipַ -osType=`cat /etc/os-release|grep ID |awk NR==1|awk -F \" '{print $2}'` -basearch=`arch` - - - -#--------------------------------# -mkdir -p $targetdir -echo install_path=$install_path >> $source_file -touch $source_file - - -#--------------------------------# -#ȫ -cd $install_path -yum -y install make gcc g++ git -yum install -y java-1.8.0-openjdk-devel.aarch64 ncurses-devel.aarch64 bzip2-devel.aarch64 python3-devel python bazel cmake3 -pip3 install tensorflow - - -function install_R-4.3.0() { - install_lapack-3.8.0 - cd $install_path - wget https://cran.r-project.org/src/base/R-4/R-4.3.0.tar.gz - tar xvf R-4.3.0.tar.gz - cd R-4.3.0 - yum install libXt-devel libX11-devel readline-devel libz bzip2-devel liblzma* xz-devel pcre-devel pcre2-devel libcurl-devel -y - ./configure --prefix=$targetdir/R_4_3_0/R_4_3_0_install - make -j - make install - echo export PATH=$targetdir/R_4_3_0/R_4_3_0_install/bin:$PATH >> $source_file - echo export LD_LIBRARY_PATH=$targetdir/R_4_3_0/R_4_3_0_install/R/library:$LD_LIBRARY_PATH >> $source_file -} - -#GSEA -function install_GSEA() { - #װjava - yum install java-11-openjdk-devel.aarch64 -y - #װӻ - #yum install xorg-x11-xauth xorg-x11-server-utils xorg-x11-server-Xnest libXtst -y - #sed -i "s/X11Forwarding no/X11Forwarding yes/g" /etc/ssh/sshd_config - #systemctl restart sshd.service - cd $install_path - wget https://data.broadinstitute.org/gsea-msigdb/gsea/software/desktop/4.3/GSEA_4.3.2.zip - unzip GSEA_4.3.2.zip - echo export PATH=$install_path/GSEA_4.3.2:\$PATH >> $source_file -} - -#pangolin -function install_pangolin() { - #װ - yum install python3-devel python3 python3-pip git make -y - cd $install_path - wget https://github.com/cov-lineages/pangolin/archive/refs/tags/v4.3.1.tar.gz -O pangolin-v4.3.1.tar.gz - tar xf pangolin-v4.3.1.tar.gz - cd pangolin-4.3.1 - pip3 install . -i https://pypi.tuna.tsinghua.edu.cn/simple - pip3 install git+https://github.com/cov-lineages/pangolin-data.git - pip3 install git+https://github.com/cov-lineages/scorpio.git - pip3 install git+https://github.com/cov-lineages/constellations.git - pip3 install snakemake -i https://pypi.tuna.tsinghua.edu.cn/simple -} - - - -#randfold -function install_randfold() { - cd $install_path - git clone https://github.com/eb00/randfold.git - cd randfold/src/squid-1.9g - ./configure && make - cd ../ - make - echo export PATH=$install_path/randfold/src >> $source_file - } - - #blat - function install_BLAT() { - cd $install_path - wget https://codeload.github.com/djhshih/blat/tar.gz/v35.1 -O blat-35.1.tar.gz - yum -y install libpng-devel - tar zxvf blat-35.1.tar.gz - cd blat-35.1/ - sed -i 's/jmp_buf htmlRecover/\/\/jmp_buf htmlRecover/g' src/inc/htmshell.h - export MACHTYPE=aarch64 - make - echo export PATH=$install_path/blat-35.1/bin:\$PATH >> $source_file -} - - -#BWA -function install_BWA() { - cd $install_path - wget https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 - tar -xvf bwa-0.7.17.tar.bz2 - cd bwa-0.7.17 && wget https://raw.githubusercontent.com/jratcliff63367/sse2neon/master/SSE2NEON.h - sed -i 's/#include /#include "SSE2NEON.h"/g' ksw.c - sed -i 's/const uint8_t rle_auxtab/\/\/const uint8_t rle_auxtab/g' rle.h |grep rle_auxtab - make - echo export PATH=$install_path/bwa-0.7.17:\$PATH >> $source_file -} - - - -#gatk -function install_gatk() { - #blat,bwa - #blat - install_BLAT - #BWA - install_BWA - #samtools - install_samtools - cd $install_path - wget https://github.com/broadinstitute/gatk/releases/download/4.0.0.0/gatk-4.0.0.0.zip -O gatk-4.0.0.0.zip - unzip gatk-4.0.0.0.zip - echo export PATH=$install_path/gatk-4.0.0.0:\$PATH >> $source_file -} - - -#Rosetta -function install_Rosetta() { - yum -y install openssl-devel - pip3 install tensorflow nltk pandas - pip3 install tensorflow Rosetta -} - -#AlphaFold -function install_AlphaFold() { - pip3 install AlphaFold -} - -#STAR -function install_star() { - cd $install_path - wget https://github.com/alexdobin/STAR/archive/refs/tags/2.7.1a.tar.gz -O STAR-2.7.1a.tar.gz - tar -xvf STAR-2.7.1a.tar.gz && cd STAR-2.7.1a - sed -i 's/\?\=/\?= \-flto \-march=native \-mcpu=tsv110/g' source/Makefile|grep ? - cd source - make STAR - echo export PATH=$install_path/STAR-2.7.1a/source/:\$PATH >> $source_file -} - -function install_gcc-9.3.1() { -#bgcc -mkdir -p $install_path/gcc -cd $install_path -wget http://mirrors.concertpass.com/gcc/releases/gcc-9.1.0/gcc-9.1.0.tar.xz -wget gcc.gnu.org/pub/gcc/infrastructure/gmp-6.1.0.tar.bz2 -wget gcc.gnu.org/pub/gcc/infrastructure/mpfr-3.1.4.tar.bz2 -wget gcc.gnu.org/pub/gcc/infrastructure/mpc-1.0.3.tar.gz -wget gcc.gnu.org/pub/gcc/infrastructure/isl-0.18.tar.bz2 - - - -#gccgmpmpfrmpcislĸ⣬mpfrgmpislgmpmpcgmpmpfr˰װgcc֮ǰȸϵΰװĸ - -tar -xvf gcc-9.1.0.tar.xz -tar -xvf gmp-6.1.0.tar.bz2 -tar -xvf mpfr-3.1.4.tar.bz2 -tar -xvf mpc-1.0.3.tar.gz -tar -xvf mpc-1.0.3.tar.gz - - -#װgmp -cd $install_path/gmp-6.1.0 -./configure --prefix=$install_path/gcc/gmp-6.1.2 -make -j64 && make install -cd .. - - -#װmpfr -cd $install_path/mpfr-3.1.4 -./configure --prefix=$install_path/gcc/mpfr-3.1.4 --with-gmp=$install_path/gcc/gmp-6.1.2 -make -j64 && make install -cd .. - -#װmpc -cd $install_path/mpc-1.0.3 -./configure --prefix=$install_path/gcc/mpc-1.0.3 --with-gmp=$install_path/gcc/gmp-6.1.2 --with-mpfr=$install_path/gcc/mpfr-3.1.4 -make -j64 && make install -cd .. - -#װisl -yum -y install gmp-devel -cd $install_path/isl-0.18 -./configure --prefix=$install_path/gcc/isl-0.18 --with-gmp=$install_path/gcc/gmp-6.1.2 --with-mpfr=$install_path/gcc/mpfr-3.1.4 --with-mpc=$install_path/gcc/mpc-1.0.3 -make -j64 && make install -cd .. - -cd $install_path/gcc-9.1.0 -mkdir gcc-build-9.1.0 -cd gcc-build-9.1.0 -rm -rf ../host-aarch64-unknown-linux-gnu -../configure --enable-checking=release --enable-languages=c,c++ --disable-multilib --prefix=$install_path/gcc/gcc-9.1.0 --with-gmp=$install_path/gcc/gmp-6.1.2 --with-mpfr=$install_path/gcc/mpfr-3.1.4 --with-mpc=$install_path/gcc/mpc-1.0.3 -make -j64 && make install -echo export PATH=$install_path/gcc/gcc-9.1.0/bin/:\$PATH >> $source_file - - -g++ --version -} - -#bgcc-10.3.1 -function install_gcc() { - cd $install_path - wget https://mirrors.huaweicloud.com/kunpeng/archive/compiler/kunpeng_gcc/gcc-10.3.1-2022.06-aarch64-linux.tar.gz - tar -xvf gcc-10.3.1-2022.06-aarch64-linux.tar.gz - cd gcc-10.3.1-2022.06-aarch64-linux - mkdir -p $targetdir/kunpeng-gcc-10.3.1 - cp -rf ./* $targetdir/kunpeng-gcc-10.3.1 - echo export PATH=$targetdir/kunpeng-gcc-10.3.1/bin:\$PATH >> $source_file - source $source_file -} - - -function install_go() { - cd $targetdir - wget https://golang.google.cn/dl/go1.18.2.linux-arm64.tar.gz - mkdir -p go_install - mv go1.18.2.linux-arm64.tar.gz ./go_install - - cd ./go_install - tar -xf go1.18.2.linux-arm64.tar.gz - yum install environment-modules -y - source /etc/profile - cat > $targetdir/go_install/go_modulefiles << EOF -#%Module1.0 -conflict go -variable modfile [file normalize [info script]] -proc getModulefileDir {} { - variable modfile - set modfile_path [file dirname $modfile] - return $modfile_path -} -set pwd [getModulefileDir] -set GO_install $pwd -setenv GO_install $GO_install -prepend-path PATH $GO_install/go/bin - -EOF - module use /usr/local/go_install/ - module load /usr/local/go_install/go_modulefiles - go version - -} - -#ncbi-vdb -function install_ncbi-vdb() { - cd $install_path - wget https://github.com/ncbi/ncbi-vdb/archive/refs/tags/3.0.0.tar.gz -O ncbi-vdb-3.0.0.tar.gz - yum -y install doxygen cmake - yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y - tar -xvf ncbi-vdb-3.0.0.tar.gz - cd ncbi-vdb-3.0.0 - cp -r interfaces/cc/gcc/arm64 interfaces/cc/gcc/aarch64 - ./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 --prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 - make -j $(nproc) && make install -} - - -#sratoolkit-3.0.0 -function install_sratoolkit() { - install_ncbi-vdb - cd $install_path - wget https://github.com/ncbi/sra-tools/archive/refs/tags/3.0.0.tar.gz -O sratoolkit-3.0.0.tar.gz - yum install wget git tar libatomic git openssl glibc-devel libstdc++-static make perl cmake fuse-devel libxml2-devel file-devel patch -y - tar zxvf sratoolkit-3.0.0.tar.gz - cd sra-tools-3.0.0 - cd tools/sharq/bm/ - wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/bmutil.h.patch - - patch -p0 < bmutil.h.patch - cd ../../../ - cd tools/copycat/ - wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/ccsra.c.patch - patch -p0 < ccsra.c.patch - cd ../../ - sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" tools/sharq/CMakeLists.txt - sed -i "s/add_definitions(-msse4.2 -DBMSSE42OPT)/ /" test/sharq/CMakeLists.txt - cd tools/driver-tool/secure/ - wget https://gitee.com/openeuler/AvxToNeon/blob/master/avx2neon.h - sed -i 's/#include /#include /' string.cpp - cd ../../../ - ./configure --relative-build-out-dir --build-prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --prefix=$targetdir/sratoolkit/sra-tools-3.0.0 --with-ncbi-vdb-prefix=$targetdir/sratoolkit/ncbi-vdb-3.0.0 - make -j $(nproc) - make install - - echo export $targetdir/sratoolkit/sra-tools-3.0.0/bin >> $source_file - -} - - -#cutadapt -function install_cutadapt() { - pip3 install cutadapt==4.1 - #pip3 install cutadapt -i http://mirrors.aliyun.com/pypi/simple/ --trusted-host mirrors.aliyun.com -} - - - -#Bowtie2 -function install_Bowtie2() { - cd $install_path - wget https://github.com/BenLangmead/bowtie2/archive/refs/tags/v2.4.1.tar.gz -O bowtie2-2.4.1.tar.gz - yum install zlib.aarch64 zlib-devel.aarch64 zlib-static.aarch64 - tar -xvf bowtie2-2.4.1.tar.gz - cd bowtie2-2.4.1 - mkdir -p third_party/simde/simde/x86/ - export NO_TBB=1 - export POPCNT_CAPABILITY=0 - wget https://codeload.github.com/simd-everywhere/simde/tar.gz/refs/tags/v0.7.6 -O simde-0.7.6.tar.gz - tar -xvf simde-0.7.6.tar.gz - - wget https://codeload.github.com/jratcliff63367/sse2neon/zip/refs/heads/master -O sse2neon.zip - - cp -a simde-0.7.6/simde third_party/simde/ - cp sse2neon-master/SSE2NEON.h sse2neon-master/sse2neon.h - cp -a sse2neon-master/sse2neon.h ./third_party/simde/simde/x86/ - make all - echo export PATH=$install_path/bowtie2-2.4.1:\$PATH >> $source_file -} - - - -#deeptool -function install_deeptool() { - cd $install_path - wget https://github.com/deeptools/deepTools/archive/refs/tags/3.5.1.tar.gz -O deepTools-3.5.1.tar.gz - tar -xvf deepTools-3.5.1.tar.gz - cd $install_path/deepTools-3.5.1 - python3 setup.py install -} - - - -#meme -function install_meme() { - cd $install_path - wget https://meme-suite.org/meme/meme-software/5.4.0/meme-5.4.0.tar.gz - tar -xvf meme-5.4.0.tar.gz - cd meme-5.4.0 - yum install -y libtool* autoconf automake nodejs* perl* libxml2* libxslt* - #cpan XML::Simple - #cpan Sys::info - #cpan Math::CDF - #cpan HTML::TreeBuilder.pm - #cpan JSON - ./configure --prefix=$targetdir/MEME - make - make install - echo export PATH=$targetdir/MEME/bin:\$PATH >> $source_file -} - - -#ncbi-blast -function install_ncbi-blast() { - cd $install_path - wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.13.0/ncbi-blast-2.13.0+-src.tar.gz -O ncbi-blast-2.13.0+-src.tar.gz - tar xzf ncbi-blast-2.13.0+-src.tar.gz - cd ncbi-blast-2.13.0+-src - export BLAST_TOP=`pwd` - export CC=gcc - export CXX=g++ - cd $BLAST_TOP - tar -xvf LMDB_0.9.24.tar.gz - cd lmdb-LMDB_0.9.24 - export LMDB_PATH=$BLAST_TOP/lmdb-LMDB_0.9.24 - cd $BLAST_TOP/c++ - ./configure - cd ReleaseMT/build - make all_r -j - make -j && make install - cd $BLAST_TOP/c++/ReleaseMT/bin - ls blastp - blastp -} - -#emboss -function install_emboss() { - cd $install_path - wget ftp://emboss.open-bio.org/pub/EMBOSS/old/6.5.0/EMBOSS-6.5.7.tar.gz - yum install -y epel-release - yum install -y gcc - yum install -y gcc-c++ - yum install -y cmake - yum install -y make - yum install -y libX11 - yum install -y libX11-devel - tar -zxvf EMBOSS-6.5.7.tar.gz - cd EMBOSS-6.5.7/ - ./configure --prefix=$targetdir/EMBOSS --build=aarch64-unknown-linux-gnu - make -j - make install - cd $targetdir/EMBOSS/bin - echo export PATH=$targetdir/EMBOSS/bin:\$PATH >> $source_file -} - -# -function install_TRF() { - cd $install_path - #git clone https://github.com/Benson-Genomics-Lab/TRF.git - wget https://github.com/Benson-Genomics-Lab/TRF/archive/refs/tags/v4.09.1.tar.gz -O TRF-4.09.1.tar.gz - tar -xvf TRF-4.09.1.tar.gz - cd TRF-4.09.1 - mkdir build - cd build - ../configure --prefix=$targetdir/RepeatMasker/TRF_install - make -j - make install -} - -#ncbi-blast-2.10.0 -function install_ncbi-blast-2.10.0() { - cd $install_path - wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-src.tar.gz - wget https://www.repeatmasker.org/rmblast/isb-2.10.0+-rmblast.patch.gz - tar -xvf ncbi-blast-2.10.0+-src.tar.gz - gunzip isb-2.10.0+-rmblast.patch.gz - cd ncbi-blast-2.10.0+-src - patch -p1 < ../isb-2.10.0+-rmblast.patch - cd c++ - wget https://gitee.com/sunlock0653/hpcrunner/raw/master/patch/B_patch.cpp - patch $install_path/ncbi-blast-2.10.0+-src/c++/src/build-system/configure ./B_patch.cpp - ./configure --with-mt --without-debug --without-krb5 --without-openssl --with-projects=scripts/projects/rmblastn/project.lst --prefix=$targetdir/rmblast/rmblast_install - make -j && make - make install -} - -#repeatmaster -function install_repeatmaster() { - install_TRF - install_ncbi-blast-2.10.0 - - yum install perl perl-CPAN -y - cd $install_path - wget http://www.repeatmasker.org/RepeatMasker/RepeatMasker-4.1.2-p1.tar.gz - tar -xvf RepeatMasker-4.1.2-p1.tar.gz - cd RepeatMasker - yum install python3 python3-pip pip3 install h5py - chmod -R 755 * - ./configure - - #²$targetdirҪ滻ɱֵ - #$targetdir/RepeatMasker/TRF_install/bin/trf - # 2 - #$targetdir/rmblast/rmblast_install/bin/ - # y - #5 - echo export PATH=$install_path/RepeatMasker:\$PATH >> $source_file -} - - - -function install_bats-0.4.0() { - cd $install_path - wget https://github.com/sstephenson/bats/archive/refs/tags/v0.4.0.tar.gz - tar -xvf v0.4.0.tar.gz - cd bats-0.4.0 - echo export PATH=$install_path/bats-0.4.0/bin:\$PATH >> $source_file -} - -function install_pygtftk-1.6.2() { - install_bats-0.4.0 - cd $install_path - wget https://github.com/dputhier/pygtftk/archive/refs/tags/v1.6.2.tar.gz - tar xvf v1.6.2.tar.gz - cd pygtftk-1.6.2 - pip3 install -r requirements.txt - pip3 install cython==0.29.30 - python3 setup.py install -} - - -function install_python-3.11.5() { - cd $install_path - wget https://www.python.org/ftp/python/3.11.5/Python-3.11.5.tar.xz - tar xvf Python-3.11.5.tar.xz - cd Python-3.11.5 - ./configure --prefix=$targetdir/python_3_11_5/python_3_11_5_install - make -j - make install - echo export PATH=$targetdir/python_3_11_5/python_3_11_5_install/bin:\$PATH >> $source_file - echo export LD_LIBRARY_PATH=$targetdir/python_3_11_5/python_3_11_5_install/lib:$LD_LIBRARY_PATH >> $source_file - echo export INCLUDE=/$targetdir/python_3_11_5/python_3_11_5_install/include:$INCLUDE >> $source_file -} - - -function install_snakemake-7.32.4() { - install_python-3.11.5 - install_BWA - install_samtools - cd $install_path - wget https://files.pythonhosted.org/packages/f4/94/884160dab89886cef7802df0a8c8217bfb2d795427dee01ad0e0dc15964a/snakemake-7.32.4.tar.gz - tar xvf v7.32.4.tar.gz - cd snakemake-7.32.4 - pip3 install . -} - -function install_lapack-3.8.0() { - cd $install_path - wget https://www.cp2k.org/static/downloads/lapack-3.8.0.tgz - tar xvf lapack-3.8.0.tgz - cd lapack-3.8.0 - cp make.inc.example make.inc - sed -i "23s/$/ -fallow-argument-mismatch/g" make.inc - sed -i "25s/$/ -fallow-argument-mismatch/g" make.inc - mkdir build - cd build - cmake .. -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=$targetdir/lapack_3_8_0/lapack_3_8_0_install - make -j - make install - echo export LD_LIBRARY_PATH=$targetdir/lapack_3_8_0/lapack_3_8_0_install/lib:$LD_LIBRARY_PATH >> $source_file -} - - - -function install_scenic-1.3.1() { - install_R-4.3.0 - cd $install_path - R -e 'install.packages("BiocManager")' - R -e 'BiocManager::install("arrow")' - R -e 'install.packages("devtools")' - R -e 'devtools::install_github("aertslab/AUCell")' - R -e 'devtools::install_github("aertslab/RcisTarget")' - R -e 'devtools::install_github("aertslab/GENIE3")' - R -e 'BiocManager::install("ggrepel")' - R -e 'devtools::install_github("aertslab/SCENIC")' -} - - -function install_uclust() { - install_R-4.3.0 - cd $install_path - R -e 'install.packages("uclust")' -} - - -function install_onemap() { - install_R-4.3.0 - cd $install_path - R -e 'install.packages("onemap", dependencies=TRUE)' -} - - -function install_poppr() { - install_R-4.3.0 - cd $install_path - R -e 'install.packages("poppr")' -} - - - -function install_seurat-5.0.0() { - install_R-4.3.0 - cd $install_path - wget https://github.com/satijalab/seurat/archive/refs/tags/v5.0.0.tar.gz - tar xvf v5.0.0.tar.gz - cd seurat-5.0.0/ - R -e 'install.packages("BiocManager")' - R -e 'BiocManager::install(c("SeuratObject", "cowplot", "fastDummies", "fitdistrplus", "future", "future.apply", "generics", "ggplot2", "ggrepel", "ggridges", "httr", "ica", "igraph", "irlba", "leiden", "lmtest", "matrixStats", "miniUI", "patchwork", "pbapply", "plotly", "png", "progressr", "RANN", "RColorBrewer", "RcppAnnoy", "RcppHNSW", "reticulate", "ROCR", "RSpectra", "Rtsne", "scales", "scattermore", "sctransform", "shiny", "spatstat.explore", "spatstat.geom", "tibble", "uwot", "RcppEigen", "RcppProgress"))' - R CMD INSTALL . -} - - -function install_reditools-2.0() { - cd $install_path - yum install environment-modules openmpi-devel -y - source /etc/profile - module load mpi/openmpi-aarch64 - git clone https://github.com/tizianoflati/reditools2.0 - cd reditools2.0 - pip3 install -r requirements.txt -} - -#װopenblas -function install_openblas() { - cd $install_path - wget https://github.com/xianyi/OpenBLAS/releases/download/v0.3.23/OpenBLAS-0.3.23.tar.gz - tar -xvf OpenBLAS-0.3.23.tar.gz - cd OpenBLAS-0.3.23 - make -j 16 ARCH=aarch64 all - make PREFIX=$targetdir/openblas/openblas_install install - echo export PATH=$targetdir/openblas/openblas_install/bin:\$PATH >> $source_file - echo export LD_LIBRARY_PATH=$targetdir/openblas/openblas_install/lib:\$LD_LIBRARY_PATH >> $source_file -} - -#װgsl -function install_gsl() { - cd $install_path - wget https://ftpmirror.gnu.org/gsl/gsl-2.7.1.tar.gz - tar -xf gsl-2.7.1.tar.gz - cd gsl-2.7.1/ - ./configure --prefix=$targetdir/gsl/gsl_install - make -j 16 - make install - echo export PATH=$targetdir/gsl/gsl_install/bin:\$PATH >> $source_file - echo export LD_LIBRARY_PATH=$targetdir/gsl/gsl_install/lib:\$LD_LIBRARY_PATH >> $source_file -} - -#װadmixtools -function install_admixtools() { - #װopenblas - install_openblas - #װgsl - install_gsl - cd $install_path - wget https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz - tar -xf v7.0.2.tar.gz - cd AdmixTools-7.0.2/src - sed -i '14d' Makefile - sed -i '18d' Makefile - sed -i "14s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile - sed -i "15s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile - make -j 16 - make install - mkdir -p $targetdir/admixtools/admixtools_install - cp -r ../bin $targetdir/admixtools/admixtools_install/bin - echo export PATH=$targetdir/admixtools/admixtools_install/bin:\$PATH >> $source_file -} - -#װEIG -function install_EIG() { - #װopenblas - install_openblas - #װgsl - install_gsl - cd $install_path - wget https://github.com/DReichLab/EIG/archive/refs/tags/v8.0.0.tar.gz - mv v8.0.0.tar.gz EIG-8.0.0.tar.gz - tar -xf EIG-8.0.0.tar.gz - cd EIG-8.0.0/src - sed -i "1s%^.*$%override CFLAGS += -I../include -I$targetdir/openblas/openblas_install/include%g" Makefile - sed -i '10d' Makefile - sed -i '12d' Makefile - sed -i "10s%^.*$%override CFLAGS += -I$targetdir/openblas/openblas_install/include -I$targetdir/gsl/gsl_install/include%g" Makefile - sed -i "11s%^.*$%override LDFLAGS += -L$targetdir/openblas/openblas_install/lib -L$targetdir/gsl/gsl_install/lib%g" Makefile - make -j 16 - make install - mkdir -p $targetdir/EIG/EIG_install - cp -r ../bin $targetdir/EIG/EIG_install - cp -r ../include $targetdir/EIG_install - echo export PATH=$targetdir/EIG_install/bin:\$PATH >> $source_file -} - -#װgdal -function install_gadl() { - cd $install_path - yum install proj proj-devel -y - wget https://download.osgeo.org/gdal/3.7.0/gdal-3.7.0.tar.xz - tar -xf gdal-3.7.0.tar.xz - cd gdal-3.7.0/ - mkdir build - cd build - cmake ../ -DCMAKE_INSTALL_PREFIX=$targetdir/gdal/gdal_install - make install - echo export PATH=$targetdir/gdal/gdal_install/bin:\$PATH >> $source_file - echo export LD_LIBRARY_PATH=$targetdir/gdal/gdal_install/lib:\$LD_LIBRARY_PATH >> $source_file -} - -#װcommot -function install_commot() { - #װ - yum install python3-devel python3 python3-pip git make -y - install_gadl - source $source_file - pip install commot -i https://pypi.tuna.tsinghua.edu.cn/simple -} - -function install_asset() { -# װ - pip3 install asset -} - - -function install_astral() { - #װ - cd $install_path - wget https://github.com/smirarab/ASTRAL/archive/refs/tags/v5.7.1.tar.gz -O ASTRAL-5.7.1.tar.gz - tar -zxf ASTRAL-5.7.1.tar.gz - cd ASTRAL-5.7.1 - sh make.sh - echo "PATH=$inspath/ASTRAL-5.7.1:$PATH" >> $source_file -} - - -function install_bayescan() { - #װ - cd $install_path - wget https://github.com/mfoll/BayeScan/archive/refs/tags/v2.1.tar.gz - tar xvf v2.1.tar.gz - cd BayeScan-2.1/ - make -j - echo "PATH=$inspath/BayeScan-2.1:$PATH" >> $source_file -} - -function install_daligner() { - #װ - cd $install_path - wget https://github.com/thegenemyers/DALIGNER/archive/refs/tags/V1.0.tar.gz -O DALIGNER-1.0.tar.gz - tar -zxf DALIGNER-1.0.tar.gz - cd DALIGNER-1.0/ - make -j - echo "PATH=$inspath/DALIGNER-1.0:$PATH" >> $source_file -} - -function install_ectools() { - #װ - cd $install_path - wget https://github.com/jgurtowski/ectools/archive/refs/tags/v0.1.tar.gz -O ectools-0.1.tar.gz - tar -xvf ectools-0.1.tar.gz - cd ectools-0.1/ - cd test - ../schtats -log -stdout test.sim.fa -} - - -function install_EVidenceModeler() { - #װ - cd $install_path - yum install -y perl perl-URI - git clone --recursive https://github.com/EVidenceModeler/EVidenceModeler.git - cd EVidenceModeler - git checkout EVidenceModeler-v2.1.0 - sed -i "s/-m64//g" `grep -rl "\-m64"` - make -j - cd testing - ./runMe.sh -} - - -function install_FASconCAT() { - #װ - cd $install_path - git clone https://github.com/PatrickKueck/FASconCAT.git - cd FASconCAT/ - echo "PATH=$inspath/FASconCAT:$PATH" >> $source_file -} - -function install_GMcloser() { - #װ - cd $install_path - wget https://sourceforge.net/projects/gmcloser/files/GMcloser-1.6.2.tar.gz - tar xvf GMcloser-1.6.2.tar.gz - cd GMcloser-1.6.2 - ./gmcloser -h -} - -function install_3d-dna() { - #װ - cd $install_path - git clone https://github.com/theaidenlab/juicer.git - cd juicer - ln -s CPU scripts - cd scripts/common - wget https://hicfiles.tc4ga.com/public/juicer/juicer_tools.1.9.9_jcuda.0.8.jar - ln -s juicer_tools.1.9.9_jcuda.0.8.jar juicer_tools.jar - cd $install_path - git clone https://github.com/theaidenlab/3d-dna.git - ./juicer/scripts/juicer.sh -h - ./3d-dna/run-asm-pipeline.sh -h -} - - - -function install_allhic() { - install_go - mkdir -p $install_path/allhic - cd $install_path/allhic - mkdir src pkg bin - export GOPATH=$install_path/allhic - go env -w GO111MODULE=on - go env -w GOPROXY=https://goproxy.cn,direct - - wget https://github.com/tanghaibao/allhic/archive/refs/tags/v0.9.13.tar.gz - tar -xf v0.9.13.tar.gz - cd $install_path/allhic/allhic-0.9.13 - go mod init allhic - go mod tidy - cd $install_path/allhic/allhic-0.9.13/cmd - go install main.go - mv $install_path/allhic/bin/main $install_path/allhic/bin/allhic - yum install environment-modules -y - source /etc/profile - cat > $install_path/allhic/allhic_modulefiles << EOF -#%Module1.0 -conflict go -variable modfile [file normalize [info script]] -proc getModulefileDir {} { - variable modfile - set modfile_path [file dirname $modfile] - return $modfile_path -} -set pwd [getModulefileDir] -set allhic $pwd -setenv allhic $allhic -prepend-path PATH $allhic/bin -EOF - - echo module use $install_path/allhic >> $source_file - echo module use $install_path/allhic/allhic_modulefiles >> $source_file - source $source_file - allhic --version - - -} - - - -function install_yass() { - cd $install_path - wget https://codeload.github.com/laurentnoe/yass/tar.gz/refs/tags/1.16_alpha1 -O yass-1.16_alpha1.tar.gz - tar -xvf yass-1.16_alpha1.tar.gz - cd yass-1.16_alpha1/ - autoreconf - ./configure --with-threads --build=aarch64-unknown-linux-gnu - automake - make - cd src - ./yass -v -} - - -function install_amas() { - cd $install_path - #װ - wget https://codeload.github.com/marekborowiec/AMAS/zip/refs/heads/master -O AMAS.zip - unzip AMAS.zip - mv AMAS-master AMAS - cd AMAS - pip install virtualenv - virtualenv AMAS - source AMAS/bin/activate - cd $install_path/AMAS/ - ls - python3 setup.py install -} - - -function install_htslib() { - cd $install_path - wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 - tar -xvf htslib-1.16.tar.bz2 - cd htslib-1.16 - yum -y install zlib-devel bzip2-devel xz-devel - ./configure - make -j - make install -} - - -function install_angsd() { - cd $install_path - install_htslib - wget http://popgen.dk/software/download/angsd/angsd0.938.tar.gz - yum -y install curl curl-devel - make HTSSRC=/usr/local/lib -} - -function install_yak() { - cd $install_path - wget https://codeload.github.com/lh3/yak/tar.gz/refs/tags/v0.1 -O yak-0.1.tar.gz - tar -xvf yak-0.1.tar.gz - cd yak-0.1/ - make -j -} - - -function install_art-nextgen-simulation-tools() { - cd $install_path - yum -y install gsl gsl-devel - wget https://mirror.tuna.tsinghua.edu.cn/raspbian/raspbian/pool/main/a/art-nextgen-simulation-tools/art-nextgen-simulation-tools_20160605%2Bdfsg.orig.tar.xz - tar -xvf art-nextgen-simulation-tools_20160605+dfsg.orig.tar.xz - cd art_src_MountRainier_Linux - autoreconf --install - ./configure --prefix=$install_path/art-nextgen-simulation-tools-install - make -j - make install -} - -function install_idba() { - cd $install_path - wget https://codeload.github.com/abishara/idba/tar.gz/refs/tags/1.1.3a1 -O idba-1.1.3a1.tar.gz - tar -xvf idba-1.1.3a1.tar.gz - cd idba-1.1.3a1/ - ./build.sh -} - - -#samtools -function install_samtools() { - #gcc-10.3.1 - cd $install_path - wget https://codeload.github.com/samtools/samtools/tar.gz/0.1.9 -O samtools-0.1.9.tar.gz - tar -xvf samtools-0.1.9.tar.gz - cd samtools-0.1.9 - make - echo export PATH=$install_path/samtools-0.1.9:\$PATH >> $source_file -} - - -function install_samtools-1.16.1() { - cd $install_path - wget https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2 - tar -xvf samtools-1.16.1.tar.bz2 - cd samtools-1.16.1 - make -j && make install -} - -function install_minimap2() { - git clone https://github.com/lh3/minimap2.git - cd minimap2/ - make arm_neno=1 aarch64=1 -} - - -function install_flye() { #bug - cd $install_path - install_gcc - git clone https://github.com/fenderglass/Flye.git - cd Flye/ - git checkout 2.3.1 - cd ./lib/minimap2 - wget https://raw.githubusercontent.com/DLTcollab/sse2neon/master/sse2neon.h - cd - - sed -i 's//\"sse2neon.h\"/g' ./lib/minimap2/ksw2_ll_sse.c - python setup.py install -} - -function install_szip() { - cd $install_path - wget https://distfiles.macports.org/szip/szip-2.1.1.tar.gz - tar xf szip-2.1.1.tar.gz - cd szip-2.1.1/ - ./configure --prefix=$install_path/sizp - make && make install -} - -function install_hdf5() { - cd $install_path - wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.12/src/hdf5-1.8.12.tar.gz - tar xf hdf5-1.8.12.tar.gz - cd hdf5-1.8.12 - ./configure --enable-cxx --enable-static=yes --enable-shared --prefix=$install_path/hdf5/hdf5-1.8.12 --build=arm LDFLAGS="-L$install_path/szip/szip-2.1.1/lib" CPPFLAGS="-I$install_path/szip/szip-2.1.1/include" - make -j - make install -} - - -function install_blasr() { - wget https://codeload.github.com/BioinformaticsArchive/blasr/zip/refs/heads/master -O blasr-master.zip - unzip blasr-master.zip - cd blasr-master/ - sed -i "5c\HDF5INCLUDEDIR=$install_path/hdf5/hdf5-1.8.12/include" common.mk - sed -i "6c\HDF5LIBDIR=$install_path/hdf5/hdf5-1.8.12/lib" common.mk - sed -i "s/\-static//g" `grep -rnl "\-static"` - sed -i "13s/$/ -ldl/" common.mk - sed -i "33s/testIn/testIn.good()/g" ./common/data/hdf/HDFFile.h - sed -i "242c\ (unsigned int) curPrefix.tuple + 1 < (unsigned int) (this->lookupTableLength));" ./common/datastructures/suffixarray/SuffixArray.h - sed -i "2271s/cout <> $source_file -} - -function install_ViennaRNA() { - cd $install_path - wget https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.4.tar.gz - tar -zxvf ViennaRNA-2.4.4.tar.gz - cd ViennaRNA-2.4.4/ - cd ViennaRNA-2.4.4 - ./configure --prefix=/path/to/ViennaRNA -build=arm-linux - make - make install -} - - - -function install_hifiasm() { - cd $install_path - git clone https://github.com/chhylp123/hifiasm.git - git clone https://github.com/DLTcollab/sse2neon.git - export C_INCLUDE_PATH=$install_path/sse2neon - export CPLUS_INCLUDE_PATH=$install_path/sse2neon - sed -i 's/#include /#include /g' ksw2_extz2_sse.c - sed -i 's/#include /#include /g' Levenshtein_distance.h - sed -i 's/#include \"smmintrin.h\"//g' Levenshtein_distance.h - sed -i 's/#include \"nmmintrin.h\"//g' Levenshtein_distance.h - sed -i 's/#include \"emmintrin.h\"//g' Levenshtein_distance.h - make -} - -yum -y install python3 python3-devel python3-pip -pip install virtualenv - - - - -function install_taxonkit() { - cd $install_path - install_go - git clone https://github.com/shenwei356/taxonkit - cd taxonkit/taxonkit/ - go build - echo export PATH=$install_path/taxonkit/taxonkit:\$PATH >> $source_file -} - - - - -function install_cdhit() { #bug - install_bisheng - wget https://github.com/weizhongli/cdhit/archive/refs/tags/V4.8.1.tar.gz - tar -xvf V4.8.1.tar.gz - cd cdhit-4.8.1 - sed -i "1,3s/g++/clang/g" Makefile - make -} - - -function install_raxml-ng() { - git clone --recursive https://github.com/amkozlov/raxml-ng.git - cd raxml-ng/ - mkdir build && cd build - cmake .. - make install -} - -function install_interval() { - cd $install_path - pip2 install docopt==0.6.2 - pip2 install pysam - git clone https://github.com/kepbod/interval.git - cd interval/ - python2 setup.py install - echo export PATH=$install_path/interval/build/lib:$PATH >> $source_file -} - - -function install_CIRCexplorer() { - cd $install_path - install_interval - wget https://github.com/YangLab/CIRCexplorer/archive/refs/tags/1.1.10.tar.gz - tar -xvf 1.1.10.tar.gz - cd CIRCexplorer-1.1.10/ - python2 setup.py install - CIRCexplorer.py -h -} - - - -function install_wise() { #bug - install_gcc - wget https://src.fedoraproject.org/repo/extras/wise2/wise2.4.1.tar.gz/d70c404c1dc40ceef7718757b11bdaa0/wise2.4.1.tar.gz - tar -xvf wise2.4.1.tar.gz - cd wise2.4.1 - cd src/ - find . -name makefile | xargs sed -i 's/glib-config/pkg-config glib-2.0/' - perl -p -i -e 's/getline/getline_ReadSeqVars/g' ./HMMer2/sqio.c - perl -p -i -e 's/isnumber/isdigit/' models/phasemodel.c - perl -p -i -e's/csh welcome.csh/sh welcome.csh/' makefile - sed -i 's/-ldyna_glib/-ldyna_glib `pkg-config --libs glib-2.0`/' models/makefile - make all -} - - -function install_beast() { - cd $install_path - wget https://github.com/CompEvol/beast2/releases/download/v2.7.0/BEAST.v2.7.0.Linux.aarch64.tgz - tar xvf BEAST.v2.7.0.Linux.aarch64.tgz - yum -y install java-devel - echo export PATH=$install_path/beast/bin/:$PATH >> $source_file -} - - - -function install_bioperl() { - pip2 install numpy - pip2 install biopython==1.76 - wget -O - https://install.perlbrew.pl | bash - cd /root/perl5/perlbrew/bin/ - ./perlbrew install-cpanm - ./cpanm install Bio::Perl -} - -function install_CPC() { - cd $install_path - install_bioperl - wget http://cpc2.gao-lab.org/data/CPC2-beta.tar.gz - tar -xf CPC2-beta.tar.gz - cd CPC2-beta/ - export CPC_HOME=`pwd` - cd libs/libsvm/ - tar -xf libsvm-3.18.tar.gz - cd libsvm-3.18/ - make - sed -i -e "s/print \(.*\)/print \(\1\)/g" ./bin/seqio.py - sed -i "s/ file(/ open(/g" ./bin/CPC2.py - python2 bin/CPC2.py -} - -function install_hpcrunner() { - cd $install_path - git clone https://gitee.com/sunlock0653/hpcrunner.git -} - -function install_CMAQ() { - install_hpcrunner - cd $install_path/hpcrunner - git checkout EA-1.0 - source ./init.sh - ./jarvis -use templates/CMAQ/5.3.1/data.CMAQ.arm_kgcc.cpu.config - ./jarvis -d - ./jarvis -dp - ./jarvis -b - - module use $install_path/hpcrunner/software/modulefiles - module purge - module load kgcc/9.3.1 - module load hmpi/1.1.1 - module load hdf5/1.10.1 - module load netcdf/4.7.0 - module load optimized-routines/20.02 - module load ioapi/3.2 -} - -function install_wavewatch() { - cd $install_path - git clone https://github.com/NOAA-EMC/WW3.git - ./model/bin/w3_setup model -c Gnu -s NCEP_st4 - export WWATCH3_NETCDF=NC4 - export NETCDF_CONFIG=`which nc-config` - - cd model/bin - ./w3_automake -} - - -function install_POM() { - install_CMAQ - module use $install_path/hpcrunner/software/modulefiles - module purge - module load kgcc/9.3.1 - module load hmpi/1.1.1 - module load hdf5/1.10.1 - module load netcdf/4.7.0 - module load optimized-routines/20.02 - module load ioapi-kgcc/3.2 - - cd $install_path - wget -r -p -k -np -nc -e robots=off http://www.ccpo.odu.edu/POMWEB/GRID-DATA - wget -r -p -k -np -nc -e robots=off http://www.ccpo.odu.edu/POMWEB/POM2K - cd $install_path/www.ccpo.odu.edu/POMWEB/POM2K - rm -rf runpom2k - wget https://gitee.com/sunlock0653/hpcrunner/raw/EA-1.0/wait_file/runpom2k - chmod 755 runpom2k - ./runpom2k -} - -function install_camx() { - wget https://www.camx.com/getmedia/CAMx_v7.20.src.220430.tgz - module use $install_path/hpcrunner/software/modulefiles - module purge - module load kgcc/9.3.1 - module load hmpi/1.1.1 - module load hdf5/1.10.1 - module load netcdf/4.7.0 - module load optimized-routines/20.02 - sed -i -e "s#\/usr\/local\/mpich3#${install_path}/hpcrunner\/software\/mpi\/hmpi1.1.1-kgcc9.3.1\/1.1.1#g" Makefile - cd ./MPI/util - sed -i -e "s#\/usr\/local\/mpich-3.0.4.pgi.2019.CE#${install_path}/hpcrunner\/software\/mpi\/hmpi1.1.1-kgcc9.3.1\/1.1.1#g" Makefile - cd - - make COMPILER=gfortran CONFIG=v7.20 MPI=mpich3 IEEE=true -} - - -function install_swan() { - install_cmake - git clone https://gitlab.tudelft.nl/citg/wavemodels/swan.git && cd swan - mkdir build && cd build - cmake .. -G Ninja - cmake --build . -} - -function install_mitgcm() { - cd $install_path - module use $install_path/hpcrunner/software/modulefiles - module purge - module load kgcc/9.3.1 - module load hmpi/1.1.1 - module load hdf5/1.10.1 - module load netcdf/4.7.0 - wget http://mitgcm.org/download/other_checkpoints/MITgcm_c67o.tar.gz - tar -xvf MITgcm_c67o.tar.gz - git clone https://gitee.com/kp-hpc-mod/hpc-patch.git - patch -p0 < hpc-patch/patch_file/MITgcm_c67o.patch - cd MITgcm - cd verification/exp4/build - ../../../tools/genmake2 -mods=../code -mpi -of=../../../tools/build_options/linux_arm64_gfortran - make depend - make -j -} - - -function create_virtualenv(){ - cd $install_path - pip3 install virtualenv -i https://pypi.tuna.tsinghua.edu.cn/simple - yum install python3 python3-devel python3-pip - python3 -m virtualenv $install_path - #pip2 install virtualenv -i https://pypi.tuna.tsinghua.edu.cn/simple - #yum install python2 python2-devel python2-pip - #python -m virtualenv $install_path - source $install_path/bin/activate -} - -function install_cpat() { - pip3 install cpat -} - -function install_CIRI() { - wget https://sourceforge.net/projects/ciri/files/CIRI2/CIRI_v2.0.6.zip - unzip CIRI_v2.0.6.zip - cd CIRI_v2.0.6/ -} - - -function install_trimmomatic() { - wget https://github.com/timflutre/trimmomatic/archive/refs/heads/master.zip - unzip master.zip.2 - cd trimmomatic-master/ - make -j - make install INSTALL=/path/to/trimmomatic-install - -} - - -function install_spliceGrapher() { - cd $install_path - wget https://master.dl.sourceforge.net/project/splicegrapher/SpliceGrapher-0.2.7.tgz - tar -xvf SpliceGrapher-0.2.7.tgz - rm -rf SpliceGrapher-0.2.7.tgz - git clone https://gitee.com/kp-hpc-mod/hpc-patch.git - patch -p0 < hpc-patch/patch_file/SpliceGrapher-0.2.7.patch - tar -zcvf SpliceGrapher-0.2.7.tgz SpliceGrapher-0.2.7 - pip3 install SpliceGrapher-0.2.7.tgz - #pip2 install SpliceGrapher-0.2.7.tgz -} - - -function install_svmu() { - wget https://codeload.github.com/mahulchak/svmu/tar.gz/refs/tags/0.3-alpha -O svmu-0.3-alpha.tar.gz - tar -xvf svmu-0.3-alpha.tar.gz - cd svmu-0.3-alpha/ - make -} - -function install_MrBayes() { - cd $install_path - wget https://codeload.github.com/NBISweden/MrBayes/tar.gz/refs/tags/v3.2.7 -O MrBayes-3.2.7.tar.gz - tar -xvf MrBayes-3.2.7.tar.gz - cd MrBayes-3.2.7/ - ./configure - make && sudo make install -} - -function install_tapis() { - create_virtualenv - install_spliceGrapher - pip3 install numpy bx-python pysam matplotlib streams -i https://pypi.tuna.tsinghua.edu.cn/simple - pip3 install django-activity-stream -i https://pypi.tuna.tsinghua.edu.cn/simple - cd $install_path - git clone https://bitbucket.org/singhbit/tapis.git - cd $install_path/tapis - python3 setup.py build - pip3 install . -} - - - -conda create -n envname python=3.8 -conda activate envname -pip3 install numpy -i https://pypi.tuna.tsinghua.edu.cn/simple -pip3 install cython -i https://pypi.tuna.tsinghua.edu.cn/simple -pip3 install mdtraj -i https://pypi.tuna.tsinghua.edu.cn/simple -pip3 install pandas>=1.4 -i https://pypi.tuna.tsinghua.edu.cn/simple -cd $install_path -git clone https://github.com/LQCT/MDScan.git -cd MDScan/ -pip3 install . -i https://pypi.tuna.tsinghua.edu.cn/simple - - - - -function install_htslib() { - yum install zlib-devel bzip2 bzip2-devel xz-devel -y - cd $install_path - wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2 - tar -jxvf htslib-1.10.2.tar.bz2 - cd htslib-1.10.2/ - ./configure --prefix=cd $install_path/htslib - make -j - make install - ln -s /usr/local/lib/libhts.so.3 /usr/lib/libhts.so.3 - sudo ldconfig -} - -function install_pindel() { - install_htslib - cd $install_path - git clone https://github.com/genome/pindel.git - cd pindel/ - ./INSTALL ../htslib-1.10.2 - ./INSTALL ../htslib-1.10.2 - ./bam2pindel.pl - -} - - - -function install_szip() { - cd $install_path - wget https://distfiles.macports.org/szip/szip-2.1.1.tar.gz - tar xf szip-2.1.1.tar.gz - cd szip-2.1.1 - ./configure --prefix=/path/to/szip - make - make install -} - -function install_networkx() { - wget https://pypi.tuna.tsinghua.edu.cn/packages/f1/8e/f6f345ed7b228d080e338eac5a6bcce2260390468ae9130dcb67096f59c4/networkx-1.1.tar.gz - tar -xvf networkx-1.1.tar.gz - cd networkx-1.1 - python setpu.py install -} - -function install_pysam() { - wget https://pypi.tuna.tsinghua.edu.cn/packages/a4/ea/901d47d5621f15c05079dcf45e746a77bab21dbf0f9ce272993a3ca3a367/pysam-0.8.0.tar.gz - tar -xvf pysam-0.8.0.tar.gz - cd pysam-0.8.0/ - python setup.py install -} - - - - - -function install_blasr() { - pip install intervaltree==2.1.0 -i https://pypi.tuna.tsinghua.edu.cn/simple - pip install intervaltree-bio==1.0.1 -i https://pypi.tuna.tsinghua.edu.cn/simple - install_networkx - pip install numpy==1.16.6 -i https://pypi.tuna.tsinghua.edu.cn/simple - pip install PyIntervalTree==0.5 -i https://pypi.tuna.tsinghua.edu.cn/simple - install_pysam - pip install PyVCF==0.6.8 -i https://pypi.tuna.tsinghua.edu.cn/simple - install_hdf5 - cd $install_path - git clone https://github.com/HWsunqian0027/blasr.git - export HDF5INCLUDEDIR= $install_path/hdf5/hdf5-1.8.12/include - export HDF5LIBDIR= $install_path/hdf5/hdf5-1.8.12/lib/ - cd blasr/ - make -} - - -function install_PBSuite() { - wget https://sourceforge.net/projects/pb-jelly/files/PBSuite_15.8.24.tgz - tar -xvf PBSuite_15.8.24.tgz - cd PBSuite_15.8.24/ - a=`pwd` - sed -i "s#SWEETPATH=.*#SWEETPATH=$a#g" setup.sh - source ./setup.sh - ./bin/Jelly.py --help -} - - - - - -function install_clustalw() { - wget http://www.clustal.org/download/current/clustalw-2.1.tar.gz - tar -xvf clustalw-2.1.tar.gz - mv config.guess config.guess_bak - mv config.sub config.sub_bak - cp /usr/share/automake-1.16/config.* . - ./configure - make -} - - - - - - - -function install_hycom() { -cd $install_path -wget https://github.com/HYCOM/HYCOM-src/releases/download/2.3.01/HYCOM-src_2.3.01.tar.gz -chsh -s /bin/csh -module use $install_path/hpcrunner/software/modulefiles -module purge -module load kgcc/9.3.1 -module load hmpi/1.1.1 -tar -xvf HYCOM-src_2.3.01.tar.gz -#wget https://gitee.com/-/ide/project/kp-hpc-mod/hpc-patch/edit/master/-/patch_file/HYCOM-src_2.3.01.patch -git clone https://gitee.com/kp-hpc-mod/hpc-patch.git -patch -p0 < hpc-patch/patch_file/HYCOM-src_2.3.01.patch -cd HYCOM-src_2.3.01/ -./Make.csh -chsh -s /bin/bash -} - - - - -#------exagear--------------------# -if [ "$1" == "bayenv2_public" ];then - git clone https://bitbucket.org/tguenther/bayenv2_public.git - ./bayenv2 -i hgdp_no_X_37_freqs -e PCs.env -m hgdp_matrix_1 -s samplesize.txt -k 10 -p 10 -fi - - -wget https://github.com/CEMPD/SMOKE/archive/refs/tags/SMOKEv5_Jun2023.tar.gz -tar -xvf SMOKEv5_Jun2023.tar.gz -cd SMOKE-SMOKEv5_Jun2023/scripts/install -chmod +x smoke_install_v47.csh -./smoke_install_v47.csh - - - - -if [ ! -n "$OPT" ]; then -install_$OPT - -else -source $source_file -fi \ No newline at end of file diff --git a/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config b/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config index 2e83460..e3b1312 100644 --- a/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config +++ b/templates/wrf/4.3.3/bisheng/data.wrf.arm.cpu.config @@ -9,32 +9,32 @@ set -e set -x module purge module use ./software/modulefiles -./jarvis -install kml/1.6.0/gcc any -./jarvis -install bisheng/2.5.0 com -module load bisheng/2.5.0 +./jarvis -install bisheng/3.2.0 com +module load bisheng/3.2.0 export CC=clang CXX=clang++ FC=flang ./jarvis -install jasper/1.900.2 clang module load jasper/1.900.2 -./jarvis -install hmpi/1.2.0 clang -module load hmpi/1.2.0 +./jarvis -install hmpi/2.3.0 clang +module load hmpi/2.3.0 export CC=mpicc CXX=mpicxx FC=mpifort ./jarvis -install hdf5/1.12.0/clang clang+mpi module load hdf5-clang/1.12.0 -./jarvis -install netcdf/4.7.4/clang clang+mpi -module load netcdf-clang/4.7.4 ./jarvis -install pnetcdf/1.12.1 clang+mpi module load pnetcdf/1.12.1 -#tar -zxvf $JARVIS_DOWNLOAD/wrf-4.3.3.tar.gz +./jarvis -install netcdf/4.8.1/clang clang+mpi +module load netcdf-clang/4.8.1 +./jarvis -install kml/2.4.0/bisheng clang +tar -zxvf $JARVIS_DOWNLOAD/wrf-4.3.3.tar.gz [ENV] #!/bin/bash module purge module use ./software/modulefiles -module load bisheng/2.5.0 +module load bisheng/3.2.0 module load jasper/1.900.2 -module load hmpi/1.2.0 -module load hdf5-clang/1.12.0 netcdf-clang/4.7.4 pnetcdf/1.12.1 -module load kml-gcc/1.6.0 +module load hmpi/2.3.0 +module load hdf5-clang/1.12.0 netcdf-clang/4.8.1 pnetcdf/1.12.1 +module load kml-bisheng/2.4.0 export WRFIO_NCD_LARGE_FILE_SUPPORT=1 export NETCDF=$NETCDF_CLANG_PATH export HDF5=$HDF5_CLANG_PATH @@ -55,18 +55,67 @@ export WRFIO_NCD_LARGE_FILE_SUPPORT=1 [APP] app_name = WRF build_dir = ${WRF_DIR} -binary_dir = +binary_dir = case_dir = ${JARVIS_ROOT}/workloads/test_wrf [BUILD] +cat << \EOF > ./arch/configure.defaults +########################################################### +#ARCH Linux aarch64,clang HYPERMPI#serial smpar dmpar dm+sm +DESCRIPTION = CLANG ($SFC/$SCC) +DMPARALLEL = 1 +OMPCPP = -D_OPENMP +OMP = -fopenmp +OMPCC = -fopenmp +SFC = flang +SCC = clang +CCOMP = clang +DM_FC = mpif90 -f90=$(SFC) +DM_CC = mpicc -cc=$(SCC) -DMPI2_SUPPORT +FC = CONFIGURE_FC +CC = CONFIGURE_CC +LD = $(FC) -L$(KML_BISHENG_PATH)/lib -lkm +RWORDSIZE = CONFIGURE_RWORDSIZE +PROMOTION = #-fdefault-real-8 +ARCH_LOCAL = -DNONSTANDARD_SYSTEM_SUBR -DWRF_USE_CLM +CFLAGS_LOCAL = -mcpu=native -w -O3 -c -march=armv8.2-a +LDFLAGS_LOCAL = +CPLUSPLUSLIB = +ESMF_LDFLAG = $(CPLUSPLUSLIB) +FCOPTIM = -O3 -march=armv8.2-a +FCREDUCEDOPT = $(FCOPTIM) +FCNOOPT = -O0 +FCDEBUG = -g # -fbacktrace -ggdb-fcheck=bounds,do,mem,pointer -ffpe-trap=invalid,zero,overflow +FORMAT_FIXED = -ffixed-form +FORMAT_FREE = -ffree-form -ffree-line-length-0 +FCSUFFIX = +BYTESWAPIO = -fconvert=big-endian +FCBASEOPTS_NO_G = -w $(FORMAT_FREE) $(BYTESWAPIO) +FCBASEOPTS = -mcpu=native $(OMP) $(FCBASEOPTS_NO_G) +MODULE_SRCH_FLAG = +TRADFLAG = -traditional +CPP = /lib/cpp -P +AR = ar +ARFLAGS = ru +M4 = m4 -G +RANLIB = ranlib +RLFLAGS = +CC_TOOLS = $(SCC) + +#insert new stanza before the Fujitsu block, keep Fujitsu at the end of the list +########################################################### +#ARCH NULL +#insert new stanza before the Fujitsu block, keep Fujitsu at the end of the list +########################################################### +#ARCH NULL +EOF echo 4 | ./configure -./compile -j 16 em_real 2>&1 | tee compile.log +./compile -j 16 em_real 2>&1 | tee compile.log [CLEAN] ./clean [RUN] run = dsub -s run.sh -binary = -nodes = 1 - +binary = +nodes = 1 \ No newline at end of file -- Gitee