Split dependencies into different environment files

[vinisalazar]

Hi,

Thank you for providing this tool. I am very excited to use it.

I am hoping to install AGNOSTOS, but I am concerned with the fact that all dependencies seem to be lumped together in the workflow.yaml file. In my experience, this can very easily lead to problems with environment setup, specially in a distributed cluster context.

Would you consider providing separate environment files for each rule/dependency? This could potentially facilitate the installation and portability of dependencies of the workflow. I would be glad to submit a PR attempting to implement this for your appreciation, since it's something I am inclined to do so I can use AGNOSTOS myself. I also believe doing this separation of dependencies into distinct files could be a step forwarding to including more tools listed in the installation_script.sh (e.g. I believe Parasail, Kaiju, EggNOG-mapper all have Bioconda distributions?).

Thank you for any assistance you can provide.

Best,
V

[AshSudarshan]

Hi! Were you able to implement this?