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covingto / pancanmafmerge

A repo for code specifically tailored to the merger of the TCGA PanCan VCF (per-caller) files into a MAF file. This repository borrows from code available in other repositories and has some custom code to handle the merger. The project's main purpose is simply to do the merge for this one project and therefore has no features to make it more generic or maintainable beyond this goal.
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Missing script? #11

Open kellrott opened 6 years ago

kellrott commented 6 years ago

The runner script seems to need a script named /stornext/snfs2/can/code/jython/jython-2.7.0/bin/jython -J-Xmx15g /hgsc_software/cancer-analysis/halotron/illumina/illumina_v0.0.2/halotron/illumina/annotation/annotate_vcf_cosmic.py but that isn't part of the repo.

covingto commented 6 years ago

added the script to the repo. looks like this is hard coded into the program.

Could you alter to reflect that jython 2.7.0 is a requirement for the project and change to reflect to the home directory of this project for the source of annotate_vcf_cosmic.py

kellrott commented 6 years ago

We're working on refactoring the different modules into a CWL/docker workflow. We'll get this script in as a tool in that chain.