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Becksteinlab / GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
https://gromacswrapper.readthedocs.org
GNU General Public License v3.0
169 stars 53 forks source link

GromacsWrapper via conda #109

Closed MamtaMohan closed 1 year ago

MamtaMohan commented 7 years ago

Hi,

Is it possible to have a conda install of GromacsWrapper?

orbeckst commented 7 years ago

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.

MamtaMohan commented 7 years ago

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

orbeckst commented 6 years ago

We should consider making a conda package for bioconda.

UPDATE:

orbeckst commented 6 years ago

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

pgbarletta commented 3 years ago

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!

orbeckst commented 3 years ago

@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.

simonbray commented 3 years ago

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.

orbeckst commented 3 years ago

@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?

simonbray commented 3 years ago

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: https://github.com/bioconda/bioconda-recipes/pull/30357

orbeckst commented 3 years ago

Thank you very much @simonbray !

orbeckst commented 1 year ago

@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.

simonbray commented 1 year ago

No problem - it looks like it was moved from bioconda to conda-forge in this PR by @njzjz: https://github.com/bioconda/bioconda-recipes/pull/37096

orbeckst commented 1 year ago

Thank you @simonbray !