cit_scripts

Run a test

$ ./Jenkins_GenpipesFull.sh -h

usage: ./Jenkins_GenpipesFull.sh create the script for genpipes, submiting them on the HPC system

   -p <pipeline1>[,pipeline2,...]       Pipeline to test, default: do them all
   -b <branch>                          Genpipe branch to test
   -c <commit>                          Hash string of the commit to test
   -s                                   generate scritp only, no HPC submit
   -u                                   update mode, do not remove latest pipeline run
   -l                                   deploy genpipe in /tmp dir 
   -a                                   list all available pipeline and exit 
   -h                                   print this help 

Add a new pipeline to the Jenkins_GenpipesFull.sh test suite

Here is a template, modify it so it can run you pipeline and add it above the # Add new test above ^^ line in the script.

pipeline=<my new pipeline>
protocol=<new protocole version> # sometime there is no protocole 

check_run "${pipeline}_${protocol}"  # If there is no protocol, execute check_run "${pipeline}"
if [[ ${run_pipeline} == 'true' ]] ; then
    # this creates the directory where the pipeline will be ran
    
    prologue "${pipeline}_${protocol}"

    generate_script ${pipeline}_${protocol}_commands.sh \
    -r $MUGQIC_INSTALL_HOME/testdata/${pipeline}/readset.${pipeline}_${protocol}.txt \
    -t ${protocol} 

    submit

fi

check_run <pipeline> check is the pipeline need to be run (used by the -p option).

prologue <folder> creates the folder where the tests for the pipeline is ran.

generate_script <script output name> [<genpipes option>, ...] will run the $pipleine.py script with the ${pipeline }.base .ini file, the local ${pipeline}.<cluster>.ini file and the cit.ini file found in the pipeline's Genpipes folder along with all , typically a reasdset input. The output script is stored int the folder created by the prologue.

submit execute the script generated by generate_script`