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nselem / orthocore

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Unable to create a functional singularity image (sif) #4

Open javibio-git opened 6 months ago

javibio-git commented 6 months ago

Hello,

I have been trying to create a singularity image to use it on our server to avoid the root privileges from docker.

Generally, creating a singularity image from docker is straight forward and for orthocore works well as it creates the sif file. The problem is that installation of dependencies fails for Gblocks, and the orthocore perl scripts.

Have you ever tried to use Singularity for this docker image? and/or Could you provide any insights on how to resolve dependency installation issues on a Singularity image?

I am attaching the commands I used to create the Singularity image:

Commands used

  1. Defined specific tmp and cache directories: export SINGULARITY_TMPDIR=/home/user/software/singularity-tmp/tmp/ export SINGULARITY_CACHEDIR=/home/user/software/singularity-tmp/cache/

  2. Pull from docker hub singularity pull orthocore.sif docker://nselem/orthocores:latest

  3. Run the container LC_ALL=C singularity shell --bind $(pwd):/usr/src/CORE orthocore.sif /bin/bash

  4. Once inside of the Singularity shell, Gblocks is not found and neither the orthocore perl scripts, i.e. scan.pl.

Thanks in advance for any help!

nselem commented 6 months ago

Hello, Thanks for trying Orthocore. I have to warn you that I haven't maintained the image in a while because now software like gethomologues is more advanced and has some of the same functions as orthocore. Having said that, I haven't tried singularity, but I have heard that Gblock has been difficult. It is even difficult for docker to work in Windows. Perhaps this issue can help you https://github.com/nselem/corason/pull/10