diff --git a/package/bwa/0.7.17/install.sh b/package/bwa/0.7.17/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..f71c6a0bb41f47289b550ce86659f7a3d6ce8030 --- /dev/null +++ b/package/bwa/0.7.17/install.sh @@ -0,0 +1,21 @@ +#download from https://github.com/jratcliff63367/sse2neon https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 +#module load bisheng2/2.1.0 +#!/bin/bash +set -x +set -e +cd ${JARVIS_TMP} +rm -rf bwa-0.7.17 sse2neon-master +tar -xvf ${JARVIS_DOWNLOAD}/bwa-0.7.17.tar.bz2 +unzip ${JARVIS_DOWNLOAD}/sse2neon.zip +cd bwa-0.7.17 +bisheng_includedir=`which clang` +bisheng_includedir=${bisheng_includedir%/*/*}/include +cp ${JARVIS_TMP}/sse2neon-master/SSE2NEON.h ${bisheng_includedir} +sed -i "1s/gcc/clang/g" Makefile +sed -i "14s%$%-I${bisheng_includedir}%g" Makefile +sed -i "29s///g" ksw.c +sed -i "33s%^%//%g" rle.h +make +mkdir -p $1/bin +cp -r ../bwa-0.7.17/* $1/bin +rm -rf ${bisheng_includedir}/SSE2NEON.h diff --git a/package/grads/2.0.a4/install.sh b/package/grads/2.0.a4/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..5d01ebf08760c8a7fbd60b52a7d6435c8a4ecac4 --- /dev/null +++ b/package/grads/2.0.a4/install.sh @@ -0,0 +1,13 @@ +#download from https://sourceforge.net/projects/opengrads/files/grads2/2.0.a4-1/grads-2.0.a4.oga.1-src.tar.gz +#!/bin/bash +set -x +set -e + +cd ${JARVIS_TMP} +rm -rf grads-2.0.a4.oga.1-src.tar.gz +tar -xvf ${JARVIS_DOWNLOAD}/grads-2.0.a4.oga.1-src.tar.gz +cd grads-2.0.a4.oga.1 +#CC=clang CXX=clang++ +./configure --prefix=$1 --build=aarch64-unknown-linux-gnu +make -j +make install diff --git a/package/hdf5/1.10.1/install.sh b/package/hdf5/1.10.1/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..738737190130a24bda1c666224e903607e73d362 --- /dev/null +++ b/package/hdf5/1.10.1/install.sh @@ -0,0 +1,13 @@ +#download from https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz +#!/bin/bash +set -x +set -e + +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/hdf5-1.10.1.tar.gz +cd hdf5-1.10.1 +#CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort -Wno-incompatible-pointer-types-discards-qualifiers +./configure --prefix=$1 --build=aarch64-unknown-linux-gnu --build=aarch64-unknown-linux-gnu --enable-fortran --enable-static=yes --enable-parallel --enable-shared CFLAGS="-O3 -fPIC -Wno-incompatible-pointer-types-discards-qualifiers -Wno-non-literal-null-conversion" FCFLAGS="-O3 -fPIC" LDFLAGS="-Wl,--build-id" +sed -i '11835c wl="-Wl,"' libtool +make -j +make install diff --git a/package/jasper/1.900.2/install.sh b/package/jasper/1.900.2/install.sh new file mode 100644 index 0000000000000000000000000000000000000000..b61c9f4ee90566784d2b71b13713204ae1b9b3b2 --- /dev/null +++ b/package/jasper/1.900.2/install.sh @@ -0,0 +1,13 @@ +#download from https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.2.tar.gz +#!/bin/bash +set -x +set -e + +cd ${JARVIS_TMP} +rm -rf jasper-1.900.2 +tar -xvf ${JARVIS_DOWNLOAD}/jasper-1.900.2.tar.gz +cd jasper-1.900.2 +#CC=clang CXX=clang++ +./configure --prefix=$1 +make -j +make install diff --git a/templates/bwa/0.7.17/data.bwa.arm.cpu.config b/templates/bwa/0.7.17/data.bwa.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..c667b95b42ee56323e471cc73aa0b167edfd0205 --- /dev/null +++ b/templates/bwa/0.7.17/data.bwa.arm.cpu.config @@ -0,0 +1,33 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +bwa/0.7.17 https://sourceforge.net/projects/bio-bwa/files/bwa-0.7.17.tar.bz2 +sse2neon/master https://github.com/jratcliff63367/sse2neon/archive/refs/heads/master.zip sse2neon.zip +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 + + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = bwa +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install bwa/0.7.17 clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/grads/2.0.a4/data.grads.arm.cpu.config b/templates/grads/2.0.a4/data.grads.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..d0db6b6976ad11d3892b088e325b7c3c197dde35 --- /dev/null +++ b/templates/grads/2.0.a4/data.grads.arm.cpu.config @@ -0,0 +1,32 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +grads/2.0.a4 https://sourceforge.net/projects/opengrads/files/grads2/2.0.a4-1/grads-2.0.a4.oga.1-src.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 + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = grads +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install grads/2.0.a4 clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/hdf5/1.10.1/data.hdf5.arm.cpu.config b/templates/hdf5/1.10.1/data.hdf5.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..b519741c5dd5cd930117bb876a39bc50b2eb0ae1 --- /dev/null +++ b/templates/hdf5/1.10.1/data.hdf5.arm.cpu.config @@ -0,0 +1,38 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +zlib/1.2.11 https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz +bisheng/2.1.0 https://mirrors.huaweicloud.com/kunpeng/archive/compiler/bisheng_compiler/bisheng-compiler-2.1.0-aarch64-linux.tar.gz +hucx/1.1.1 https://github.com/kunpengcompute/hucx/archive/refs/tags/v1.1.1-huawei.zip hucx-1.1.1-huawei.zip +xucg/1.1.1 https://github.com/kunpengcompute/xucg/archive/refs/tags/v1.1.1-huawei.zip xucg-1.1.1-huawei.zip +hmpi/1.1.1 https://github.com/kunpengcompute/hmpi/archive/refs/tags/v1.1.1-huawei.zip hmpi-1.1.1-huawei.zip + +[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 purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=mpicc CXX=mpicxx FC=mpifort F77=mpifort + +[APP] +app_name = hdf5 +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install hdf5/1.10.1 clang + +[RUN] +run = +binary = +node = 1 diff --git a/templates/jasper/1.900.2/data.jasper.arm.cpu.config b/templates/jasper/1.900.2/data.jasper.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..a1d15ae28b90f6575bf2806545b377be4c77bba4 --- /dev/null +++ b/templates/jasper/1.900.2/data.jasper.arm.cpu.config @@ -0,0 +1,31 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +jasper/1.900.2 https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.2.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 + +[ENV] +module purge +module use ${JARVIS_ROOT}/software/modulefiles +module add bisheng2/2.1.0 +export CC=clang CXX=clang++ FC=flang + +[APP] +app_name = jasper +build_dir = ${JARVIS_ROOT} +binary_dir = +case_dir = + +[BUILD] +./jarvis -install jasper/1.900.2 clang + +[RUN] +run = +binary = +node = 1