Installing NGS_DNA pipeline

This is the Quickstart tutorial. When there are any problems, please 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 using the following command:

module load EasyBuild
eb NGS_DNA-3.5.2.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 manually download and copy the sources to ${HPC_ENV_PREFIX}/sources/[a-z]/NameOfTheSoftwarePackage/. For further details, please check install page

Run the script NGS_resources to install the required resources and create the directory structure. You can download the scripts here.

bash makestructure.sh
bash 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

1) Copy rawdata to rawdata ngs folder
scp –r 198210_SEQ_RUNTEST_FLOWCELLXX username@yourcluster:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/

2) Create a folder in the generatedscripts folder
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun

3) Copy samplesheet to generatedscripts folder
scp –r TestRun.csv username@yourcluster:/groups/$groupname/${tmpDir}/generatedscripts/

4) Run the generate script
module load NGS_DNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_DNA/generate_template.sh .
bash generate_template.sh
cd scripts

Note: If you want to run the pipeline locally, you should change the backend in the CreateInhouseProjects.sh script (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

bash submit.sh

navigate to jobs folder (this will be outputted at the step before this one).

bash submit.sh