The docker image is for a perl script to do gene fusion called soafuse.
Input files located at:
~ /hg19-GRCh37/
Normally, it can be run as:
docker run -v ~/hg19-GRCh37/:/sf -i -t bianxi/soapfuse-ref hg19 /sf/cytoBand.txt /sf/hgnc.txt /sf/hg19.fa /sf/hg.gtf
From the documentation and tutorials on Firecloud, it seems I cannot run this way, but need to first create a container and then run the script within container, which can be like the following:
docker run -v "$HOME"/hg19-GRCh37/:/sf -it --entrypoint=/bin/bash avkitex/soapfuse-ref #create container and mount ~/hg19-GRCh37 as /sf/
./constructBase.sh hg19 /sf/cytoBand.txt /sf/hgnc_complete_set.txt /sf/hg19.fa /sf/Homo_sapiens.gtf #run the script
There are two questions I’d like to have you help me with:
1. How do I pass the parameters to mount the local directory to the container so input files can be access within container?
2. How to run the command in the WDL file?