diff --git a/package/boost-python/1.72.0/install.sh b/package/boost-python/1.72.0/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..ae2843d5f1079054144a6fcb1c206b5e03833a96 --- /dev/null +++ b/package/boost-python/1.72.0/install.sh @@ -0,0 +1,11 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u https://archives.boost.io/release/1.72.0/source/boost_1_72_0.tar.gz +cd ${JARVIS_TMP} +rm -rf boost_1_72_0 +tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz +cd boost_1_72_0 +sed -i '60s/.*/#ifdef PTHREAD_STACK_MIN/' ./boost/thread/pthread/thread_data.hpp +./bootstrap.sh --with-python=`which python3` +./b2 cxxflags="$(python3-config --includes) -Wno-deprecated-builtins -Wno-enum-constexpr-conversion -fPIC" linkflags="$(python3-config --ldflags)" install --prefix=$1 diff --git a/package/boost/1.72.0/install.sh b/package/boost/1.72.0/install.sh index 0c8a87c23bd4e3f8b4c0d065f6a3bce4a7aaada5..ef7f6266da54c3ee0b93d351904aaabad161fdd3 100755 --- a/package/boost/1.72.0/install.sh +++ b/package/boost/1.72.0/install.sh @@ -1,7 +1,8 @@ #!/bin/bash set -x set -e -. ${DOWNLOAD_TOOL} -u https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz +. ${DOWNLOAD_TOOL} -u https://archives.boost.io/release/1.72.0/source/boost_1_72_0.tar.gz +#https://boostorg.jfrog.io/artifactory/main/release/1.72.0/source/boost_1_72_0.tar.gz cd ${JARVIS_TMP} rm -rf boost_1_72_0 tar -xvf ${JARVIS_DOWNLOAD}/boost_1_72_0.tar.gz diff --git a/package/samtools/1.10/install.sh b/package/samtools/1.10/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..0b9d4a75fcd3385d44b17ba103be455caa21426f --- /dev/null +++ b/package/samtools/1.10/install.sh @@ -0,0 +1,14 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2 +cd ${JARVIS_TMP} +tar xvf ${JARVIS_DOWNLOAD}/samtools-1.10.tar.bz2 +cd samtools-1.10 +./configure --prefix=$1 +make all all-htslib +make install install-htslib +mkdir $1/include/bam +cp *.h $1/include/bam +cp *.a $1/lib + diff --git a/templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config b/templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..44f5da5405379d315f5eaca54858bbc38a288a97 --- /dev/null +++ b/templates/cufflinks/2.2.1/data.cufflinks.arm.cpu.config @@ -0,0 +1,66 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +cufflinks/2.2.1 $JARVIS_PROXY/cole-trapnell-lab/cufflinks/archive/refs/tags/v2.2.1.tar.gz cufflinks-2.2.1.tar.gz + +[DEPENDENCY] +set -e +set -x +./jarvis -install kgcc/10.3.1 com +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` + +./jarvis -install boost/1.72.0 gcc +./jarvis -install samtools/1.10 gcc +./jarvis -install eigen3/3.4.0 gcc + +module use ./software/modulefiles +module load boost/1.72.0 +module load samtools/1.10 +module load eigen3/3.4.0 + +rm -rf cufflinks-2.2.1 +tar -xzvf ${JARVIS_DOWNLOAD}/cufflinks-2.2.1.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load boost/1.72.0 +module load samtools/1.10 +module load eigen3/3.4.0 +cd ${JARVIS_ROOT}/software/libs/kgcc10.3.1/eigen3/3.4.0/include +cp -rf eigen3/Eigen . + +[APP] +app_name = cufflinks +build_dir = ${JARVIS_ROOT}/cufflinks-2.2.1 +binary_dir = +case_dir = + +[BUILD] +sed -i '16s/^/#/' configure.ac +autoreconf --install +sed -i 's/-lbam/-lbam -lhts/g' configure +sed -i 's/#include /#include/g' src/biascorrection.h +sed -i 's/hash\[pos\].hash/(hash\[pos\].hash)/g' src/GHash.hh +sed -i '70s/return;/return *this;/;72s/return;/return *this;/' src/lemon/error.h +sed -i 's/curwin/curwins/g' src/locfit/c_plot.c +./configure --with-boost=${BOOST_PATH} --with-eigen=${EIGEN3_PATH} --with-bam=${SAMTOOLS_PATH} +make +make install + +[CLEAN] +make clean + +[RUN] +run = +binary = +nodes = 1 + + diff --git a/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config b/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config new file mode 100644 index 0000000000000000000000000000000000000000..8a13cf7ec0407929428d0c80c3b471c5cc84b386 --- /dev/null +++ b/templates/ecFlow/5.5.2/data.ecFlow.arm.cpu.config @@ -0,0 +1,64 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +ecFlow/5.5.2 https://confluence.ecmwf.int/download/attachments/8650755/ecFlow-5.5.2-Source.tar.gz + +[DEPENDENCY] +set -e +set -x +./jarvis -install kgcc/10.3.1 com +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +export CC=`which gcc` +export CXX=`which g++` +export FC=`which gfortran` + +yum install -y python3 +yum install -y qt5 qt5-devel + +./jarvis -install boost-python/1.72.0 gcc + +rm -rf ecFlow-5.5.2-Source +tar -xzvf ${JARVIS_DOWNLOAD}/ecFlow-5.5.2-Source.tar.gz + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +#module load boost-python/1.72.0 + +[APP] +app_name = ecFlow +build_dir = +binary_dir = +case_dir = + +[BUILD] +export BOOST_ROOT=${JARVIS_TMP}/boost_1_72_0 +export WK=${JARVIS_ROOT}/ecFlow-5.5.2-Source +export BOOST_PATH=${JARVIS_ROOT}/software/libs/kgcc10.3.1/boost-python/1.72.0 + +cd ${JARVIS_TMP}/boost_1_72_0 +$WK/build_scripts/boost_build.sh + +cd ${WK} +mkdir build +cd build +cmake .. -DENABLE_UI=ON -DENABLE_PYTHON=ON -DBoost_INCLUDE_DIR=${BOOST_PATH}/include -DCMAKE_CXX_FLAGS="-Wno-enum-constexpr-conversion -fPIC" -DBoost_PYTHON3_LIBRARY_RELEASE=${BOOST_PATH}/lib/libboost_python39.a -DBoost_PYTHON_LIBRARY_RELEASE=${BOOST_PATH}/lib/libboost_python39.a +make +make install + +[CLEAN] +make clean + +[RUN] +run = +binary = +nodes = 1 + +[PERF] +perf= +nsys= +ncu=--target-processes all