Modular system to create reports from metadata and workflow output, see more at ReadTheDocs.
The software in this directory contains plugins to djerba specific to PanCuRx and LBR at OICR.
To enter the djerba environment on the OICR cluster, start with:
qrsh -P pcsi -l h_vmem=10G
module load djerba
export DJERBA_PRIVATE_DIR=/.mounts/labs/PCSI/users/
export DJERBA_SOURCE_DIR=/.mounts/labs/PCSI/users/fbeaudry/djerba-pancurx
Next, you'll need to make .INI file that contains the parameters of your djerba run. At the very least, the minimal INI should look like:
[core]
[sample_helper]
donor = BTC0025
tumour=BTC_0025_Sn_M_526
normal=BTC_0025_Ly_R
[file_helper]
[pancurx.summary]
[pancurx.somatic]
[pancurx.germline]
[pancurx.classification]
[pancurx.all_genes]
[pancurx.appendix]
[pancurx.slide]
where square brackets (e.g. [pancurx.summary]) indicate the specific plugins to run. If you do not wish to print the entire djerba report, it is possible to run djerba with only a subset of the plugins.
Within a pluging, parameters are set by naming the parameter, putting an = sign and then followed by the value for the parameter. In the above, all values are left default except in the sample_helper plugin which requires the donor id, tumour sample id, and normal id. Many more parameters can be specified when necessary.
Finally, you can launch djerba with the following command to first make the report (report), then make a .pdf of the report (render):
python3 ${DJERBA_SOURCE_DIR}/src/bin/djerba.py --debug report --ini config.ini --out-dir report --no-archive
python3 ${DJERBA_SOURCE_DIR}/src/bin/djerba.py render --json report/report.json --out-dir report --pdf --no-archive
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Licensed under the GPL 3.0 license.