diff --git a/package/bamtools/2.5.0/install.sh b/package/bamtools/2.5.0/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..8fb49d335794aa3b7c2f26ec4869cf5f9468653a --- /dev/null +++ b/package/bamtools/2.5.0/install.sh @@ -0,0 +1,13 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.0.tar.gz -f bamtools-2.5.0.tar.gz +cd ${JARVIS_TMP} +rm -rf bamtools-2.5.0 +tar -xvf ${JARVIS_DOWNLOAD}/bamtools-2.5.0.tar.gz +cd bamtools-2.5.0 +export CC=clang CXX=clang++ FC=flang +mkdir build && cd build +cmake -DCMAKE_INSTALL_PREFIX=$1 .. -DCMAKE_CXX_FLAGS="-std=c++14 -O3" .. +make -j +make install diff --git a/package/boost/1.72.0/clang/install.sh b/package/boost/1.72.0/clang/install.sh index 9f61ca81ae0c8bd6cd0cd98ef7d12d58a9cf2526..06b1f1ef729abee386d42bcf739cb7eef4e88171 100755 --- a/package/boost/1.72.0/clang/install.sh +++ b/package/boost/1.72.0/clang/install.sh @@ -6,5 +6,5 @@ cd ${JARVIS_TMP} tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz cd boost_1_72_0 sed -i '60s/.*/#ifdef PTHREAD_STACK_MIN/' ./boost/thread/pthread/thread_data.hpp -./bootstrap.sh --with-toolset=clang +./bootstrap.sh --with-toolset=clang --with-libraries=system,serialization,program_options ./b2 toolset=clang cxxflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" linkflags="-std=c++14 -stdlib=libc++ -Wno-error=enum-constexpr-conversion" install --prefix=$1 \ No newline at end of file diff --git a/package/mysql/3.3.0/install.sh b/package/mysql/3.3.0/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..8b02cebca6158afc851d9656a970ed6609b12f81 --- /dev/null +++ b/package/mysql/3.3.0/install.sh @@ -0,0 +1,10 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://tangentsoft.com/mysqlpp/releases/mysql++-3.3.0.tar.gz +cd ${JARVIS_TMP} +rm -rf mysql++-3.3.0 +tar -xvf ${JARVIS_DOWNLOAD}/mysql++-3.3.0.tar.gz +cd mysql++-3.3.0 +./configure --prefix=$1 +make -j && make install diff --git a/package/petsc/3.19.6/install.sh b/package/petsc/3.19.6/install.sh index 5e1e96876ed6457d906d2fc40fa48f94e9685ba7..5f6c49c21c001a39efebc08b965a104934b1a1d1 100755 --- a/package/petsc/3.19.6/install.sh +++ b/package/petsc/3.19.6/install.sh @@ -2,12 +2,13 @@ set -x set -e . ${DOWNLOAD_TOOL} -u https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.19.6.tar.gz +. ${DOWNLOAD_TOOL} -u https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.11/src/hdf5-1.10.11.tar.bz2 cd ${JARVIS_TMP} rm -rf petsc-3.19.6 tar -xvf ${JARVIS_DOWNLOAD}/petsc-3.19.6.tar.gz cd petsc-3.19.6 ./configure F77=$F77 --prefix=$1 --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpifort \ - --download-parmetis=1 --download-metis=1 \ - --download-hdf5=${JARVIS_DOWNLOAD} --force + --download-parmetis=1 --download-metis=1 \ + --download-hdf5=${JARVIS_DOWNLOAD}/hdf5-1.10.11.tar.bz2 --force make PETSC_DIR=${JARVIS_TMP}/petsc-3.19.6 PETSC_ARCH=arch-linux-c-debug all -j -make PETSC_DIR=${JARVIS_TMP}/petsc-3.19.6 PETSC_ARCH=arch-linux-c-debug install -j +make PETSC_DIR=${JARVIS_TMP}/petsc-3.19.6 PETSC_ARCH=arch-linux-c-debug install -j \ No newline at end of file diff --git a/templates/augustus/3.3.3/data.augustus.arm.cpu.config b/templates/augustus/3.3.3/data.augustus.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..d715359c8676853f62a33ea72b3510a50d4b7cb2 --- /dev/null +++ b/templates/augustus/3.3.3/data.augustus.arm.cpu.config @@ -0,0 +1,71 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +augustus/3.3.3 https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v3.3.3.tar.gz Augustus-3.3.3.tar.gz + +[DEPENDENCY] +set -x +set -e +yum install gsl* mysql-devel sqlite* suitesparse* -y +pip3 install parallel_augustus -i https://mirrors.aliyun.com/pypi/simple +. ${DOWNLOAD_TOOL} -u https://rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-5.5.2.5-5.mga9.aarch64.rpm +. ${DOWNLOAD_TOOL} -u https://www.rpmfind.net/linux/mageia/distrib/9/aarch64/media/core/release/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm +. ${DOWNLOAD_TOOL} -u http://bioinf.uni-greifswald.de/augustus/datasets/sag178.fa.gz +rpm -ivh ./${JARVIS_DOWNLOAD}/lpsolve-5.5.2.5-5.mga9.aarch64.rpm ./${JARVIS_DOWNLOAD}/lpsolve-devel-5.5.2.5-5.mga9.aarch64.rpm + +module purge +module use ./software/modulefiles + +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +export CC=clang CXX=clang++ FC=flang +./jarvis -install mysql/3.3.0 clang +./jarvis -install boost-clang/1.72.0 clang +./jarvis -install htslib/1.15 clang +./jarvis -install samtools/1.15 clang +./jarvis -install bamtools/2.5.0 clang + +tar -zxvf $JARVIS_DOWNLOAD/Augustus-3.3.3.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load mysql/3.3.0 +module load boost-clang/1.72.0 +module load htslib/1.15 +module load samtools/1.15 +module load bamtools/2.5.0 + +[APP] +app_name = Augustus +build_dir = ${JARVIS_ROOT} +binary_dir = ${JARVIS_ROOT}/Augustus-3.3.3/install-3.3.3/bin +case_dir = ${JARVIS_ROOT}/Augustus-3.3.3/run + +[BUILD] +rm -rf Augustus-3.3.3 +tar -zxvf ${JARVIS_DOWNLOAD}/Augustus-3.3.3.tar.gz +cd Augustus-3.3.3 + +AUGUSTUS_PATH=$(realpath ./install) +sed -i "s|\/opt\/augustus|$AUGUSTUS_PATH|g" Makefile + +make -j CC=clang CXX=clang++ \ + CFLAGS="-DCOMPGENEPRED -g -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" \ + CXXFLAGS="-DCOMPGENEPRED -g -std=c++17 -lstdc++ -I${BAMTOOLS_PATH}/include/bamtools -I${BOOST_CLANG_PATH}/include -I${HTSLIB_PATH}/include/htslib -I${MYSQL_PATH}/include/mysql++ -L${BAMTOOLS_PATH}/lib64 -L${BOOST_CLANG_PATH}/lib -L${HTSLIB_PATH}/lib -L${MYSQL_PATH}/lib -L/usr/lib64/mysql" +make install + +mkdir run +cd ./run +cp ${JARVIS_DOWNLOAD}/sag178.fa.gz . +gzip -d sag178.fa.gz + +[CLEAN] +make clean + +[RUN] +run = time -p +binary = parallel_augustus -g sag178.fa -o sag178.res -c 1024 -p 128 --extra '--species=human -UTR=on' +nodes = 1