https://github.com/afrendeiro/pipelines/ is deprecated!
https://github.com/epigen/open_pipelines/ for NGS pipelines and https://github.com/epigen/looper/ for a pipeline/job submission engine/managerSee
Clone the repository
git clone firstname.lastname@example.org:afrendeiro/pipelines.git cd pipelines
python setup.py install
pip install .
If not root, add the
--user to either command to install to your home directory.
Dependencies will be installed as well if these are not met.
You'll have now a
ngsProject command in your
ngsProject -h to see all options.
Additionally, you'll also have a
.pipeline_config.yaml file in your
$HOME upon installation.
.pipeline_config.yaml in your
$HOME contains configurations that are read by the pipeline objects.
A thorough description of the recognised configurations will soon follow.
Sample annotation sheet
The sample annotation sheet is a csv file containing sample annotation. It is passed as argument to
Columns recognized are:
cellLine, numberCells, technique, ip, patient, patientID, sampleID, treatment, biologicalReplicate, technicalReplicate, experimentName, genome, unmappedBam, but others might be present as well.