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!!

[ljw20180420]

I fork #113 and build a sif image.

$ apptainer shell oras://ghcr.io/ljw20180420/fithichip:v0.0.1

[IanCodes]

I fork #113 and build a sif image.

$ apptainer shell oras://ghcr.io/ljw20180420/fithichip:v0.0.1

Will the command line result in a SIF file? I started this running and have the message "INFO: Downloading oras image", but no files have been created after 6 hours.

[owlang]

I would just create a free account on sylabs then copy the .def file from the PR into their build tool and click "build." It shouldn't take more than 20 min or so iirc. If you're building a container on an under-resourced machine, it will take a long time and possibly error out before it finishes. The .sif build on Sylabs should then be downloadable and you can copy it to whichever machine you want to run it on. Lmk any errors you run into with the .def file but i hardened the versions so you shouldn't encounter any build issues.

I would not count on .sif files being perpetually hosted on these remote systems unless there is an active developer team tied to the project bc lots of these orgs have storage limits associated with free accounts and these images tend to get deleted sooner or later to make room on individual accounts.

[ljw20180420]

I fork #113 and build a sif image.
$ apptainer shell oras://ghcr.io/ljw20180420/fithichip:v0.0.1

Will the command line result in a SIF file? I started this running and have the message "INFO: Downloading oras image", but no files have been created after 6 hours.

No. I have built the .sif file and push it to oras://ghcr.io/ljw20180420/fithichip:v0.0.1. Run the command

$ apptainer shell oras://ghcr.io/ljw20180420/fithichip:v0.0.1

will download the .sif image and start it. There will be a prompt Apptainer> which means you are in the container environment. fithichip is available in the container. For example,

$ apptainer shell oras://ghcr.io/ljw20180420/fithichip:v0.0.1
Apptainer> ./FitHiChIP_HiCPro.sh -C configfile_BiasCorrection_CoverageBias

[IanCodes]

Thank you @owlang and @ljw20180420.

Before I saw your replies I was able to get the sif file using:
apptainer pull --disable-cache fithichip.sif oras://ghcr.io/ljw20180420/fithichip:v0.0.1

and then run it using:
singularity run --bind <path> <path>/fithichip.sif <path>_config.txt

I have output but haven't had chance to look at it yet.