diff --git a/templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config b/templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config new file mode 100644 index 0000000000000000000000000000000000000000..c7405b76a7ec0e2f9ea33e61f3a789167a4b11cc --- /dev/null +++ b/templates/velvet/1.2.10/velvet.arm.kgcc.hmpi.config @@ -0,0 +1,45 @@ +[SERVER] +11.11.11.11 + +[DOWNLOAD] +velvet/1.2.10 ${JARVIS_PROXY}/dzerbino/velvet/archive/refs/tags/v1.2.10.tar.gz velvet-1.2.10.tgz + +[DEPENDENCY] +module purge +module use ./software/modulefiles +./jarvis -install kgcc/10.3.1 com +module load kgcc/10.3.1 +./jarvis -install hmpi/2.4.2 gcc +module load hmpi/2.4.2 + +tar -zxvf ${JARVIS_DOWNLOAD}/velvet-1.2.10.tgz -C ${JARVIS_TMP_DOWNLOAD} +mkdir -p ${JARVIS_ROOT}/software/apps/velvet/bin + +[ENV] +module purge +module use ./software/modulefiles +module load kgcc/10.3.1 +module load hmpi/2.4.2 +export OMP_NUM_THREADS=96 +export OMP_THREAD_LIMIT=95 + +[APP] +app_name = velvet +build_dir = ${JARVIS_TMP_DOWNLOAD}/velvet-1.2.10 +binary_dir = ${JARVIS_ROOT}/software/apps/velvet/bin +case_dir = ${JARVIS_TMP_DOWNLOAD}/velvet-1.2.10 + +[BUILD] +sed -ri 's/\-m64/\-mabi=lp64/g' Makefile +sed -ri 's/CC = gcc/CC = mpicc/g' Makefile +sed -ri 's/CC = gcc/CC = mpicc/g' contrib/MetaVelvet-v0.3.1/Makefile +make 'GATEGORIES=10' 'MAXKMERLENGTH=57' 'LONGSEQUENCES=1' 'OPENMP=1' 'BUNDLEDZLIB=1' +cp -ar velveth velvetg ${JARVIS_ROOT}/software/apps/velvet/bin +mkdir -p ${JARVIS_TMP_DOWNLOAD}/velvet-1.2.10/output + +[CLEAN] + +[RUN] +run = ${JARVIS_ROOT}/software/apps/velvet/bin/velveth output 31 -shortPaired -fastq.gz tests/read1.fq.gz -shortPaired -fastq.gz tests/read2.fq.gz && +binary = velvetg output -min_contig_lgth 100 -cov_cutoff 9 +nodes = 1