diff --git a/package/bedtools/2.28.0/install.sh b/package/bedtools/2.28.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..ff99268b456c9e431dfa5d5a86adb22ca90bbcc6 --- /dev/null +++ b/package/bedtools/2.28.0/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash + +#wget https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz +set -x +set -e +cd ${JARVIS_TMP} +rm -rf bedtools2 +tar -zxvf ${JARVIS_DOWNLOAD}/bedtools-2.28.0.tar.gz +cd bedtools2 +sed -i '23c export CXX = clang++' Makefile +sed -i '25c CC = clang' src/utils/htslib/Makefile +make -j4 +cp -a bin/ $1 diff --git a/package/curl/7.82.0/install.sh b/package/curl/7.82.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..d57c5811139679884a4262c220b23721f31c43a3 --- /dev/null +++ b/package/curl/7.82.0/install.sh @@ -0,0 +1,16 @@ +#!/bin/bash +#https://github.com/curl/curl/releases/download/curl-7_82_0/curl-7.82.0.tar.gz +set -x +set -e +cd ${JARVIS_TMP} +rm -rf curl-7.82.0 +tar -xvf ${JARVIS_DOWNLOAD}/curl-7.82.0.tar.gz +cd curl-7.82.0 +./buildconf +./configure --prefix=$1 --without-ssl +make +make install + + + + diff --git a/package/openjpeg/2.4.0/install.sh b/package/openjpeg/2.4.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..1324c478edd384f2d06742b70084d77ee4423ea7 --- /dev/null +++ b/package/openjpeg/2.4.0/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash +#https://github.com/uclouvain/openjpeg/archive/refs/tags/v2.4.0.tar.gz +set -x +set -e +cd ${JARVIS_TMP} +rm -rf openjpeg-2.4.0 +tar -xvf ${JARVIS_DOWNLOAD}/openjpeg-2.4.0.tar.gz +cd openjpeg-2.4.0 +mkdir build +cd build +cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$1 +make install + diff --git a/package/picard/2.27.0/install.sh b/package/picard/2.27.0/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..6c4d0e5e191240f17acf61b8873641ac3c38380a --- /dev/null +++ b/package/picard/2.27.0/install.sh @@ -0,0 +1,14 @@ +#!/bin/bash +#yum install -y git java-1.8.0-openjdk +set -x +set -e +cd ${JARVIS_TMP} +rm -rf picard +git config --global --add core.compression -1 +git config --global http.sslVerify False +git clone https://github.com/broadinstitute/picard.git +cd picard +./gradlew shadowJar +cp -a build/ $1 + + diff --git a/package/pnetcdf/1.11.2/install.sh b/package/pnetcdf/1.11.2/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..58fc7d123ef3a75baa9059543b1287bf93eae270 --- /dev/null +++ b/package/pnetcdf/1.11.2/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +#http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/pnetcdf-1.11.2.tar.gz +set -x +set -e +cd ${JARVIS_TMP} +tar zxvf ${JARVIS_DOWNLOAD}/pnetcdf-1.11.2.tar.gz +cd pnetcdf-1.11.2 +#./configure --prefix=$1 --build=aarch64-linux --enable-shared --enable-fortran --enable-large-file-test CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort +./configure --prefix=$1 --build=aarch64-linux --enable-shared --enable-fortran --enable-large-file-test +make -j16 +make install diff --git a/templates/bedtools/2.28.0/data.bedtools.arm.cpu.config b/templates/bedtools/2.28.0/data.bedtools.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..b5a5d2333c32ae5552296f504337f084497e6048 --- /dev/null +++ b/templates/bedtools/2.28.0/data.bedtools.arm.cpu.config @@ -0,0 +1,40 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +hucx/1.1.1 https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.tar.gz hucx-1.1.1-huawei.tar.gz +xucg/1.1.1 https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.tar.gz xucg-1.1.1-huawei.tar.gz +hmpi/1.1.1 https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.tar.gz hmpi-1.1.1-huawei.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +bedtools/2.28.0 https://github.com/arq5x/bedtools2/releases/download/v2.28.0/bedtools-2.28.0.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install hmpi/1.1.1 clang +module load hmpi1/1.1.1 + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng2/2.1.0 +module load hmpi1/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort + +[APP] +app_name = bedtools +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +./jarvis -install bedtools/2.28.0 bisheng+mpi + +[RUN] +run = +binary = +node = 1 + diff --git a/templates/curl/7.82.0/data.curl.arm.cpu.config b/templates/curl/7.82.0/data.curl.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..39ff9ad40fc906bbc7dc3a21f7e0ad8d3bb270e3 --- /dev/null +++ b/templates/curl/7.82.0/data.curl.arm.cpu.config @@ -0,0 +1,37 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +curl/7.82.0 https://github.com/curl/curl/releases/download/curl-7_82_0/curl-7.82.0.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = curl +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +./jarvis -install curl/7.82.0 bisheng + +[RUN] +run = +binary = +node = 1 + + + + diff --git a/templates/openjpeg/2.4.0/data.openjpeg.arm.cpu.config b/templates/openjpeg/2.4.0/data.openjpeg.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..656c87d4df3e20b1c28f48a7fd90aaf9389f501b --- /dev/null +++ b/templates/openjpeg/2.4.0/data.openjpeg.arm.cpu.config @@ -0,0 +1,33 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +openjepg/2.4.0 https://github.com/uclouvain/openjpeg/archive/refs/tags/v2.4.0.tar.gz openjpeg-2.4.0.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng2/2.1.0 +export CC=clang CXX=clang FC=flang + +[APP] +app_name = openjpeg +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +./jarvis -install openjpeg/2.4.0 bisheng + +[RUN] +run = +binary = +node = 1 diff --git a/templates/picard/2.27.0/data.picard.arm.cpu.config b/templates/picard/2.27.0/data.picard.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..f4e094583f00cd54f1122df70ba2bcd6af6ba32b --- /dev/null +++ b/templates/picard/2.27.0/data.picard.arm.cpu.config @@ -0,0 +1,33 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = picard +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +./jarvis -install picard/2.27.0 bisheng + +[RUN] +run = +binary = +node = 1 + diff --git a/templates/pnetcdf/1.11.2/data.lapack.arm.cpu.config b/templates/pnetcdf/1.11.2/data.lapack.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..882575058b2a62e217f042edfafc2420d2001a41 --- /dev/null +++ b/templates/pnetcdf/1.11.2/data.lapack.arm.cpu.config @@ -0,0 +1,39 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +lapack/3.8.0 http://www.netlib.org/lapack/lapack-3.8.0.tar.gz +hucx/1.1.1 https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.tar.gz hucx-1.1.1-huawei.tar.gz +xucg/1.1.1 https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.tar.gz xucg-1.1.1-huawei.tar.gz +hmpi/1.1.1 https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.tar.gz hmpi-1.1.1-huawei.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install hmpi/1.1.1 clang +module load hmpi1/1.1.1 + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng2/2.1.0 +module load hmpi1/1.1.1 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = lacack +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +./jarvis -install lapack/3.8.0/bisheng clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/pnetcdf/1.11.2/data.pnetcdf.arm.cpu.config b/templates/pnetcdf/1.11.2/data.pnetcdf.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..af0b1578a0668c095138b5ffe10dd6dc8bccb61a --- /dev/null +++ b/templates/pnetcdf/1.11.2/data.pnetcdf.arm.cpu.config @@ -0,0 +1,43 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +hucx/1.1.1 https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.tar.gz hucx-1.1.1-huawei.tar.gz +xucg/1.1.1 https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.tar.gz xucg-1.1.1-huawei.tar.gz +hmpi/1.1.1 https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.tar.gz hmpi-1.1.1-huawei.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +pnetcdf/1.11.2 http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/pnetcdf-1.11.2.tar.gz + + +[DEPENDENCY] +module use ./software/modulefiles +module purge +./jarvis -install bisheng/2.1.0 com +module load bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install hmpi/1.1.1 clang +module load hmpi1/1.1.1 + +[ENV] +module use ./software/modulefiles +module purge +module load bisheng2/2.1.0 +module load hmpi1/1.1.1 +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort + +[APP] +app_name = pnetcdf +build_dir = $JARVIS_ROOT +binary_dir = +case_dir = + +[BUILD] +./jarvis -install pnetcdf/1.11.2 bisheng+mpi + +[RUN] +run = +binary = +node = 1 + + +