Bioconda version?

[dkoslicki]

Given many cluster environments don't play well with Docker, are there any plans to put CAMISIM on Bioconda? @abremges @AlphaSquad @alicemchardy I have a student who can assist with this if you'd like help.

[AlphaSquad]

Sounds like a good idea - and any help is greatly appreciated!

[paulzierep]

We would also love to include camisim in Galaxy. So I am starting the work for the bioconda build: bioconda/bioconda-recipes#49699

[paulzierep]

It seems, that my bold approach to add the scripts to the package bin as attempted will not work.
To put CAMISIM into bioconda I think the following steps will be required.

• Use tools from conda instead of directly using the binaries
• Make this a pip package
• Move extra files such as the .hmm profiles into a dedicated folder that can be downloaded by the tool.

If you want to follow this approach, let me know and I can further try to push this into bioconda.

[AlphaSquad]

Thank you for looking into this. We are currently developing a new version of CAMISIM using nextflow, this should also make it easier to incorporate into other workflows and conda. This version is already in a beta state, you could already try if incorporation of the dev branch works in theory - this is how CAMISIM will look in the not far future