Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Migrate aggregation script to SLURM #15

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Migrate aggregation script to SLURM #15

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 6 additions & 6 deletions scripts/aggregate.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ source ${scriptDir}/../isl/lib/functions.sh

studyId=$1
organism="homo_sapiens"
lsfMem=${2:-4096}
slurmMem=${2:-4096}

check_variables 'studyId'

Expand Down Expand Up @@ -89,25 +89,25 @@ echo $libraryPathsForStudy > $aux
# Submit aggregation to cluster

aggrCmd="irap_single_lib2report_atlas -B -j 4 folders_file=$aux out=$ISL_WORKING_DIR/studies/$studyId/$organism name=$studyId"
isl_lsf_submit 'aggregate' ${studyId}.${organism} "/irap_gtex" $lsfMem 1 $ISL_WORKING_DIR "$aggrCmd"
isl_slurm_submit 'aggregate' ${studyId}.${organism} "/irap_gtex" $slurmMem 1 $ISL_WORKING_DIR "$aggrCmd"

if [ $? -ne 0 ]; then
echo "[ERROR] Failed to submit to lsf job: '$aggrCmd'"
echo "[ERROR] Failed to submit to Slurm job: '$aggrCmd'"
exit 1
else
echo "Submitted aggregation for ${studyId} ${organism}"

# Monitor aggregation job
monitorLogPrefix=$(get_log_prefix processing 'aggregate' ${studyId}.${organism})
monitorLog="${monitorLogPrefix}.log"
isl_lsf_monitor 'aggregate' 1 $monitorLog
isl_slurm_monitor 'aggregate' 1 $monitorLog

# Once done, move to the fg_atlas ISL studies dir.
if [ $? -ne 0 ]; then
echo "LSF processing completed with errors"
echo "SLURM processing completed with errors"
exit 1
else
echo "LSF processing completed, no errors"
echo "SLURM processing completed, no errors"

# Move results to results directory
resultsDir=$(process_results_dir $studyId aggregate $organism 'no')
Expand Down