Optional parameter to disable checking for HiCPro

[jeremyd85]

I am following the HiChIP docs. I am wanting to run all these processes with just having Docker and Singularity installed on the lab computer. When running FitHiChIP_Singularity.sh it requires that HiCPro is installed on the host in order to run even though the Docker image that is in this repo installs HiCPro. This is only the case if there is a valid pairs file listed in the configuration.

The process that I am using appears to "fake" the output of HiCPro for the valid pairs file: https://hichip.readthedocs.io/en/latest/loops.html#workflow

Would it be acceptable that these scripts drop the requirement for HiCPro to be installed or would it be possible to add an option to run without HiCPro. An option could either be added to the existing config or it could be a flag added to the scripts (--skip-hicpro-check)

[ay-lab]

Hi @jeremyd85 Thanks for your query. I've updated the Docker and Singularity containers. Please download the latest code from GitHub and give it a try. Please let me know if it solves your problem.

[evaham1]

Hello! I believe I am running into the same issue as described above, I would like to run FitHiChip using just Singularity installed on our HPC, however when I run the script FitHiChIP_Singularity.sh it stops with this message:

================ Verifying input configuration parameters =================
***** Specified output directory : ../../output/NF-hichip/NF_FitHiChiP_r1
====>>> User did not provide any file in the COOL= option or the HIC= option or the Bed= option of the configuration file
==>>> So, the input interaction file is from the HiC-pro (valid pairs format)
==>>> But the matrix and bin interval files (HiC-pro) are not provided  - we need to generate them from HiC-pro
which: no HiC-Pro in (/camp/apps/eb/software/Anaconda3/2020.07/bin:/camp/apps/eb/software/Anaconda3/2020.07/condabin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/camp/home/hamrude/.local/bin:/camp/home/hamrude/bin)
ERROR ===>>>> HiC-pro is not installed in the system - FitHiChIP quits !!!

I am not sure why this check is for packages installed on the host system, should they be checking that HiCPro is installed in the Singularity container instead? Or have I misunderstood the check? Any help appreciated thank you!

[ay-lab]

Hi @jeremyd85 and @evaham1 The Docker and Singularity versions need to be updated. Please use the GitHub source code and installation instructions in the Documentation (https://ay-lab.github.io/FitHiChIP/html/usage/installation.html)