Loading launch_universc.sh +53 −2 Original line number Diff line number Diff line Loading @@ -40,7 +40,15 @@ fi #####locate launch_universc.sh, barcode sources, and other tools###### SOURCE="${BASH_SOURCE[0]}" echo "script running in $(realpath $0)..." SOURCE=${BASH_SOURCE[0]} # check if script is started via SLURM or bash (job ID defined in Slurm job) if [[ -n $SLURM_JOB_ID ]]; then if [[ $(echo $SLURM_JOB_ID | wc -w) -ge 1 ]]; then # check the original location through scontrol and $SLURM_JOB_ID SOURCE=$(scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}') fi fi SDIR="" RDIR="" Loading @@ -56,6 +64,7 @@ while [[ -h "$SOURCE" ]]; do #resolve $SOURCE until the file is no longer a syml fi done SDIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" echo "... script called from ${SDIR}" RDIR="$( dirname "$SOURCE" )" if [[ $RDIR != $SDIR ]]; then Loading Loading @@ -1937,7 +1946,6 @@ else barcodefile=${whitelistdir}/SmartSeq2_full_barcodes.txt elif [[ "$technology" == "smartseq3" ]]; then barcodefile=${whitelistdir}/SmartSeq3_full_barcodes.txt fi elif [[ "$technology" == "strt-seq" ]]; then barcodefile=${whitelistdir}/STRTSeq_barcode.txt elif [[ "$technology" == "strt-seq-c1" ]]; then Loading Loading @@ -2630,6 +2638,49 @@ fi #####checking job scheduler#### # check if cluster mode enabled if [[ ${jobmode} != "local" ]]; then echo "running in cluster mode ${jobmode}" if [[ -d $(dirname ${cellrangerpath})/martian-cs/*/jobmanagers ]]; then cd $(dirname ${cellrangerpath})/martian-cs/*/jobmanagers if [[ -f ${jobmode}.template ]]; then echo "cluster mode configured for ${jobmode}:" $(realpath ${jobmode}.template) else echo "attempting to use default template for cluster mode ${jobmode}" # copies default job template for SGE, Slurm, etc. if [[ -f ${jobmode}.template.example ]]; then cp -v ${jobmode}.template.example ${jobmode}.template fi echo "WARNING: if this does not work as expected, configure the scheduler by editing:" echo $(realpath ${jobmode}.template) fi #return to previus directory cd - fi if [[ -d $(dirname ${cellrangerpath})/external/martian/jobmanagers ]]; then cd $(dirname ${cellrangerpath})/external/martian/jobmanagers if [[ -f ${jobmode}.template ]]; then echo "cluster mode configured for ${jobmode}:" $(realpath ${jobmode}.template) else echo "attempting to use default template for cluster mode ${jobmode}" # copies default job template for SGE, Slurm, etc. if [[ -f ${jobmode}.template.example ]]; then cp -v ${jobmode}.template.example ${jobmode}.template fi echo "WARNING: if this does not work as expected, configure the scheduler by editing:" echo $(realpath ${jobmode}.template) fi #return to previus directory cd - fi else echo "running in local mode (no cluster configuration needed)" fi ######## #####exiting when setup is all that is requested##### if [[ $setup == "true" ]]; then lock=`cat $lockfile` Loading Loading
launch_universc.sh +53 −2 Original line number Diff line number Diff line Loading @@ -40,7 +40,15 @@ fi #####locate launch_universc.sh, barcode sources, and other tools###### SOURCE="${BASH_SOURCE[0]}" echo "script running in $(realpath $0)..." SOURCE=${BASH_SOURCE[0]} # check if script is started via SLURM or bash (job ID defined in Slurm job) if [[ -n $SLURM_JOB_ID ]]; then if [[ $(echo $SLURM_JOB_ID | wc -w) -ge 1 ]]; then # check the original location through scontrol and $SLURM_JOB_ID SOURCE=$(scontrol show job $SLURM_JOBID | awk -F= '/Command=/{print $2}') fi fi SDIR="" RDIR="" Loading @@ -56,6 +64,7 @@ while [[ -h "$SOURCE" ]]; do #resolve $SOURCE until the file is no longer a syml fi done SDIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )" echo "... script called from ${SDIR}" RDIR="$( dirname "$SOURCE" )" if [[ $RDIR != $SDIR ]]; then Loading Loading @@ -1937,7 +1946,6 @@ else barcodefile=${whitelistdir}/SmartSeq2_full_barcodes.txt elif [[ "$technology" == "smartseq3" ]]; then barcodefile=${whitelistdir}/SmartSeq3_full_barcodes.txt fi elif [[ "$technology" == "strt-seq" ]]; then barcodefile=${whitelistdir}/STRTSeq_barcode.txt elif [[ "$technology" == "strt-seq-c1" ]]; then Loading Loading @@ -2630,6 +2638,49 @@ fi #####checking job scheduler#### # check if cluster mode enabled if [[ ${jobmode} != "local" ]]; then echo "running in cluster mode ${jobmode}" if [[ -d $(dirname ${cellrangerpath})/martian-cs/*/jobmanagers ]]; then cd $(dirname ${cellrangerpath})/martian-cs/*/jobmanagers if [[ -f ${jobmode}.template ]]; then echo "cluster mode configured for ${jobmode}:" $(realpath ${jobmode}.template) else echo "attempting to use default template for cluster mode ${jobmode}" # copies default job template for SGE, Slurm, etc. if [[ -f ${jobmode}.template.example ]]; then cp -v ${jobmode}.template.example ${jobmode}.template fi echo "WARNING: if this does not work as expected, configure the scheduler by editing:" echo $(realpath ${jobmode}.template) fi #return to previus directory cd - fi if [[ -d $(dirname ${cellrangerpath})/external/martian/jobmanagers ]]; then cd $(dirname ${cellrangerpath})/external/martian/jobmanagers if [[ -f ${jobmode}.template ]]; then echo "cluster mode configured for ${jobmode}:" $(realpath ${jobmode}.template) else echo "attempting to use default template for cluster mode ${jobmode}" # copies default job template for SGE, Slurm, etc. if [[ -f ${jobmode}.template.example ]]; then cp -v ${jobmode}.template.example ${jobmode}.template fi echo "WARNING: if this does not work as expected, configure the scheduler by editing:" echo $(realpath ${jobmode}.template) fi #return to previus directory cd - fi else echo "running in local mode (no cluster configuration needed)" fi ######## #####exiting when setup is all that is requested##### if [[ $setup == "true" ]]; then lock=`cat $lockfile` Loading
