ro-crate-py
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ResearchObject
Distribution request: rocrate-py on conda forge
(Requested duplicate to https://github.com/ResearchObject/ro-crate/issues/217)
As an academic distributing software, I've just found myself making a conda environment (instead of a pip requirements.txt file). I'd like to be able to conda install -c conda-forge rocrate instead of:
dependencies:
- python=3.10
- pip
- pip:
- "rocrate"
A search https://anaconda.org/search?q=rocrate doesn't show rocrate as available inside the anaconda ecosystem.
Conda distributions tend to be more useful when the package has non-Python dependencies, e.g. C/C++, as is often the case for packages including extension modules. ro-crate-py, OTOH, is pure Python. That being said, Conda packages would still be nice to have, though the recipe requires work and then there's the burden of maintenance. I think the main hurdle would be the dependency from galaxy2cwl, which is not available from conda-forge.
Volunteers?
Several months ago I made a contribution to bioconda, a conda channel more biased to life sciences. I contributed the Python crypt4gh conda recipe, inspired in the public indications from an Spanish colleague (sorry, instructions are in Spanish).
But, I guess the right conda channel should be bioconda instead of conda-forge. The main reason is that one of the rocrate-py dependencies is galaxy2cwl, which does not have conda package yet (as @simleo rightly pointed out). Exploring galaxy2cwl dependencies, it depends on gxformat2, which is already at bioconda channel.
Bioconda instead of conda-forge is entirely acceptable for my needs, if that helps @jmfernandez.
ro-crate is not a life-science library, so should really be on conda-forge.
We had Gromacs in bioconda (maintained by UNIMAN for a while) and then moved it to CondaForge as it was also used by Material Sciences.
Can the galaxy2cwl dependency be optional somehow in Conda?
I think we can make galaxy2cwl an optional dependency. Without it one would be able to do everything except generating abstract CWL from Galaxy workflows.
Instead of galaxy2cwl could we not use gxformat2 directly? It can also convert to abstract CWL with gxwf-abstract-export command
https://github.com/galaxyproject/gxformat2
Just to add to the motivation: rocrate is a dependency of galaxy-data and so the the galaxy-data recipe in bioconda would like to require it at runtime - that's not possible while there isn't a conda-forge or bioconda package.
