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Becksteinlab / GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

Home Page:https://gromacswrapper.readthedocs.org

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GromacsWrapper via conda

MamtaMohan opened this issue · comments

commented

Hi,

Is it possible to have a conda install of GromacsWrapper?

commented

In principle this shouldn't be a problem – @ianmkenney has some experience.

It's just a matter of someone spending the time to create the conda package. If you have any experience with it (or just want to learn how to do it) you are more than welcome to submit a PR.

As an example you can look at MDAnalysis/GridDataFormats and its meta.yaml file. See http://docs.continuum.io/conda/build.html for more information about meta.yaml.

We'd be happy to put a package on https://anaconda.org/becksteinlab or eventually onto conda-forge.

commented

Dear Oliver,

Thank you for your response. I think it is good suggestion.

I have no experience but like to give it a try. It will take me a bit with lot going on. In my opinion conda updates are very clean and easy to manage in their own environment.

Mamta

commented

We should consider making a conda package for bioconda.

UPDATE:

commented

I created a fork for the bioconda-recipes: https://github.com/Becksteinlab/bioconda-recipes

commented

Hi, sorry to revive this issue, but I was wondering if there is a reason why conda is no longer supported.

I'm using conda, since I think it's a better option than pip+virtualenv and I wanted to add GromacsWrapper to my project.

Thanks!

commented

@pgbarletta , we never had conda packages for GromacsWrapper. I agree that it would be nice to have. It's just that nobody has gotten around to create the package. If you want to help out you're more than welcome!

Instead of bioconda I would just go with conda-forge.

commented

I went ahead and created a package, please feel free to try:

conda install GromacsWrapper -c conda-forge -c bioconda

I agree conda-forge would be preferable, but given that GROMACS itself is only available via bioconda at the minute, I went for bioconda.

commented

@simonbray fantastic (and you also packaged numkit!) — thank you!

Could you post the links to the recipes, please?

I noticed that GROMACS is a dependency. Often users will have a custom compiled version of GROMACS that they want GW to pick up (eg on a supercomputer). Is there a way to make the GROMACS conda package optional/not automatically installed so that it won't collide with the custom version?

commented

You're welcome!

Could you post the links to the recipes, please?

They are hosted on bioconda's recipes repo here:

I noticed that GROMACS is a dependency. Often users will have a custom compiled version of GROMACS that they want GW to pick up (eg on a supercomputer). Is there a way to make the GROMACS conda package optional/not automatically installed so that it won't collide with the custom version?

That is a good point. I created a PR to remove gromacs from the dependencies list here: bioconda/bioconda-recipes#30357

commented

Thank you very much @simonbray !

commented

@simonbray sorry to ping you here, I'd like to trigger a 0.8.3 for the conda package but I can't find the GromacsWrapper bioconda recipe https://github.com/bioconda/bioconda-recipes/blob/master/recipes/gromacswrapper/meta.yaml anymore. There still exists https://anaconda.org/bioconda/gromacswrapper . Any hints would be welcome! Thanks.

commented

No problem - it looks like it was moved from bioconda to conda-forge in this PR by @njzjz: bioconda/bioconda-recipes#37096