Run
scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX [email protected]:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
scp –r TestRun.csv [email protected]:/groups/$groupname/${tmpDir}/generatedscripts/
Note: the name of the folder should be the same as samplesheet (.csv) file
module load NGS_DNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_DNA/generate_template.sh .
sh generate_template.sh
cd scripts
Note: if you want to run locally, you should change in the CreateInhouseProjects.sh script the backend (this can be done almost at the end of the script where you have something like: sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh search for –b slurm and change it into –b localhost
sh submit.sh
navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).
sh submit.sh
Last modified 4yr ago