Docker image for running command line tools

[FranceCosta]

Hi MolProbity team!
I am interested in running some of the command line tools you provide and in particular "oneline-analysis" in an HPC cluster. To do so I need a docker image that I can convert to a singularity image and run from the cluster. Do you have available image in Docker-hub I can use for this purpose? Or do you have instructions to create one?

[chrissciwilliams]

Hi! Unfortunately, we do not have a Docker image available at this time. We will discuss whether we can generate one (it's a good idea), but we are a small lab right now, so I can't promise we'll find the time. To do a "regular" MolProbity installation, use the install_via_bootstrap.py script, and the instructions in the readme. The most significant, unusual dependency is an old version of PHP (conveniently packaging that with MolProbity is one of the reasons Docker would be nice). Good luck, and sorry I couldn't be more help right now, -Christopher Williams ---Richardson Lab, Duke University

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On Mon, Sep 4, 2023 at 7:04 AM Francesco Costa ***@***.***> wrote: Hi MolProbity team! I am interested in running some of the command line tools you provide and in particular "oneline-analysis" in an HPC cluster. To do so I need a docker image that I can convert to a singularity image and run from the cluster. Do you have available image in Docker-hub I can use for this purpose? Or do you have instructions to create one? — Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ACLEREEADHAIJYDB4LIFD2TXYWYTJANCNFSM6AAAAAA4KHZZCY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[FranceCosta]

Thank you Christopher for your answer. Which version of PHP would be better having? I will try creating an image.

[smlewis]

With the caveat that this was a "do once, get it working, don't touch it" kind of job - so no promises that it still works - we got MP dockerized for some purposes here: https://github.com/CyrusBiotechnology/MolProbity/blob/master/Dockerfile

This repo should be public so you should be able to grab that file as a starting point. I looked at the merge to this repo and it's not in conflict but it smells a little funny with files added, so you might want to cherry pick instead (or, just grab the file and play with it directly).

[aozalevsky]

@FranceCosta @smlewis another option is a singularity container.

Here is an example: Singularity.def

arthur@flute:~$: singularity build molprobity.sif Singularity.def
arthur@flute:~$: singularity exec --pid molprobity.sif molprobity.molprobity 4PRF.pdb

============================== Collecting inputs ==============================


                   ----------Processing PDB file(s)----------                  

As a bonus: .sif is just a binary image that can be easily transferred/copied to other machines with singularity.

NB: it takes ~20 minutes on a decent workstation to build the image on 4 cores (as recommended for the bootstrap installation).

[FranceCosta]

In case this could be useful, I converted @aozalevsky singularity recipe to a docker one. I find it handy for creating singularity images on my institute's computing cluster avoiding permission issues.