thejacksonlaboratory / cloudneo

CWL implementation of CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens

CloudNeo Workflow Overview

Overview

This repository has the CWL implementation of CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigen. The workflow was developed on Seven Bridges Genomics' CGC platfrom in CWL- Draft2 version. The CGC went live in Nov 2015 when the CWL specifications were still in Draft 2. There are differences between the draft-2 and the version v.1.0 but CGC is still in CWl-Draft2 version as of March 2017.

Running the CloudNeo workflow

• For running CloudNeo on CGC, please refer to this manual.
• For running CloudNeo CWL with Rabix, please refer to this wiki.

cloudneo's Issues

cannot create fastq: Permission denied

HI,

#The output of log:

[2018-11-15 10:59:53.710] [INFO] Job root.samtools_fastq has started
[2018-11-15 10:59:54.686] [INFO] Job root.Variant_Effect_Predictor has started
[2018-11-15 10:59:54.946] [ERROR] Job 3cf1bfc7-5fac-4f89-9d65-b9abaf9c11ac failed with exit code 2.
[2018-11-15 10:59:54.948] [INFO] Job 3cf1bfc7-5fac-4f89-9d65-b9abaf9c11ac failed with exit code 2.
[2018-11-15 10:59:55.669] [INFO] Failed to execute a Job

#I checked the error log
/bin/sh: 1: cannot create B10-B.sorted.rmdup.addhead.fastq: Permission denied

Thanks !

Baifeng

Corrections needed to rabix installation instructions

I'm currently working on setting up CloudNeo for use with rabix, and I wanted to let you know that the installation instructions need updating.

For the netMHC and netMHCpan installations, the softwares should be downloaded to the main CloudNeo directory in order to use the recommended docker image build commands as specified in the wiki (which need a '-f' in front of the docker file paths, too).

This command within the Dockerfile for each of these tools was also giving me trouble:

RUN apt-get install -y python-biopython

but I was able to use

RUN wget https://bootstrap.pypa.io/get-pip.py

RUN python get-pip.py

RUN pip install biopython

instead, and it worked fine. Not sure if this is an issue on my end or a more general issue, though.

The polysolver build also requires a lot of files that aren't in the repository and must be tracked down (e.g. GATK v3.5 jar, mutect jar, etc.).

It's fairly doable to figure out these issues out on your own, but it would be good to have more accurate and thorough instructions in the wiki.