tutorial_local_singularity.md

Tutorial for general UNIX computers with singularity

1. Git clone this pipeline and move into it.

   $ git clone https://github.com/ENCODE-DCC/hic-pipeline
   $ cd hic-pipeline

2. Install Caper, requires Python > 3.4.1

   $ pip install caper

3. CHECK YOUR SINGULARITY VERSION FIRST AND UPGRADE IT TO A VERSION >=2.5.2 OR PIPELINE WILL NOT WORK CORRECTLY.

   $ singularity --version

4. Run a pipeline for the test sample.

   $ INPUT=examples/template_one.json
   $ PIPELINE_METADATA=metadata.json
   $ caper run workflow/main_workflow/hic.wdl --use-singularity -i ${INPUT} -m ${PIPELINE_METADATA}

5. You will be able to find all outputs on cromwell-executions/hic/[RANDOM_HASH_STRING]/. See output directory structure for details.

6. See full specification for input JSON file.