NGS_DNA
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Quickstart

Installing NGS_DNA pipeline

This is the Quick tutorial, when there are problems first go to the detailed install page or when there are problems running the pipeline
We first have to load EasyBuild, this can be done with this command
module load EasyBuild
eb NGS_DNA-3.4.4.eb --robot -–robot-paths=${pathToMYeasybuild}/easybuild-easyconfigs/easybuild/easyconfigs/:
Note: some software cannot be downloaded automagically due to for example licensing or technical issues and the build will fail initially. In these cases you will have to download manually and copy the sources to ${HPC_ENV_PREFIX}/sources/[a-z]/NameOfTheSoftwarePackage/ for more details check install page
Run the script NGS_resources to install the required resources and create directory structure, you can download the scripts here
sh makestructure.sh
sh NGS_DNA-resources.sh
Note: Sometimes the GATK ftp server can be down/instable, try it a couple of times

Preparing and running NGS_DNA pipeline

scp –r 198210_SEQ_RUNTEST_FLOWCELLXX [email protected]:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
scp –r TestRun [email protected]:/groups/$groupname/${tmpDir}/generatedscripts/
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 (this will be outputted at the step before this one).
sh submit.sh