Usage with Docker

[roddypr]

Hi,

I am having difficulties installing the software. The script FitHiChIP_Docker.sh includes these these lines:

HiCProExec=`which HiC-Pro`
if [[ -z $HiCProExec ]]; then
	echo 'ERROR ===>>>> HiC-pro is not installed in the system - FitHiChIP quits !!!'
	exit 1
fi

Am I understanding it correctly that the FitHiChip Docker image needs a system-wide installation of HiC-Pro to work?

[owlang]

@roddypr I also ran into challenges with running this software last week so I built a container with singularity (not Docker, sorry). Since it was a bit fussy to build, i committed the .def file to the repo - see most recent PR (#113).

If you have singularity on your systems, you could build the image on sylabs and run it yourself. Hopefully the help and labels in the .def make the usage clear (it differs slightly from the sh FitHiChIP_Singularity.sh execution style). Hopefully you or someone else finds this convenient.

[roddypr]

Thank you so much, this is really great.

In the end, a colleague managed to run FitHiChip with Docker by changing the FitHiChIP_HiCPro.sh slightly to be compatible with the Docker container and not using the FitHiChIP_Docker.sh wrapper. This is such a hacky solution that it is not worth sharing.

In the future, I will probably have to run FitHiChip using on a HPC (i.e., with Singularity), so I will use your container!

Thanks so much for sharing your work with the community!!