diff --git a/package/htslib/1.21/clang/install.sh b/package/htslib/1.21/clang/install.sh new file mode 100755 index 0000000000000000000000000000000000000000..e90e5495a7b9675d833fa6d4a64d9a7d5f0acc97 --- /dev/null +++ b/package/htslib/1.21/clang/install.sh @@ -0,0 +1,12 @@ +#!/bin/bash +set -x +set -e +. ${DOWNLOAD_TOOL} -u $JARVIS_PROXY/samtools/htslib/releases/download/1.21/htslib-1.21.tar.bz2 +cd ${JARVIS_TMP} +tar -xvf ${JARVIS_DOWNLOAD}/htslib-1.21.tar.bz2 +yum install -y autoconf +cd htslib-1.21/ +autoreconf -i +./configure --prefix=$1 CPPFLAGS='-foverflow-shift-alt-behavior' +make -j +make install diff --git a/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config b/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config new file mode 100755 index 0000000000000000000000000000000000000000..a68a3faa4af3fc1e2ae3d9e3bf8330881ff741a9 --- /dev/null +++ b/templates/kallisto-bustools_python/0.51.1/kallisto.arm.bisheng.hmpi.config @@ -0,0 +1,49 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +kallisto/0.51.1 ${JARVIS_PROXY}/pachterlab/kallisto/archive/refs/tags/v0.51.1.tar.gz kallisto-0.51.1.tar.gz + +[DEPENDENCY] +set -e +yum install -y zlib-devel +module purge +module use ./software/modulefiles +./jarvis -install bisheng/4.1.0 com +module load bisheng/4.1.0 +./jarvis -install hmpi/2.4.2 bisheng +module load hmpi/2.4.2 +./jarvis -install hdf5/1.12.1/clang bisheng+mpi +module load hdf5-clang/1.12.1 + +mkdir -p ${JARVIS_ROOT}/software/apps/kallisto +tar -zxf ${JARVIS_DOWNLOAD}/kallisto-0.51.1.tar.gz -C ${JARVIS_TMP_DOWNLOAD} + +[ENV] +module purge +module use ./software/modulefiles +module load bisheng/4.1.0 +module load hmpi/2.4.2 +module load hdf5-clang/1.12.1 + +[APP] +app_name = kallisto +build_dir = ${JARVIS_TMP_DOWNLOAD}/kallisto-0.51.1 +binary_dir = ${JARVIS_ROOT}/software/apps/kallisto/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/kallisto-0.51.1/test + +[BUILD] +mkdir build +cd build/ +sed -i '/--disable-libcurl/s/$/\ CPPFLAGS=-foverflow-shift-alt-behavior/' ../CMakeLists.txt +cmake .. -DCMAKE_INSTALL_PREFIX=${JARVIS_ROOT}/software/apps/kallisto -DUSE_HDF5=ON -DUSE_BAM=ON +make +make install + +[CLEAN] +make clean + +[RUN] +run = ${JARVIS_ROOT}/software/apps/kallisto/bin/kallisto index -i transcripts.idx transcripts.fasta.gz && +binary = kallisto quant -i transcripts.idx -o reads-ouput -b 100 reads_1.fastq.gz reads_2.fastq.gz && head -n 20 reads-ouput/abundance.tsv +nodes = 1