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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
113 stars 25 forks source link

Script availability in conda recipe #94

Closed mbhall88 closed 2 years ago

mbhall88 commented 2 years ago

Hey,

There is a bioconda package for mccortex, which is great. But the scripts, such as make-pipeline.pl are not on PATH. If I (or yourselves) were to update the bioconda recipe to add these to the package, which scripts do you think would be necessary?

winni2k commented 2 years ago

Glad to hear that the conda package has found other users than myself!

Why not at all the scripts? I didn't include them at the time because i had no use for them, but others might.

mbhall88 commented 2 years ago

Sure. I guess the only thing will be updating the dependencies for the recipe. At a quick glance some scripts needs Perl, some need graphviz, some need python (and associated libraries), some need R...

winni2k commented 2 years ago

Yikes, sounds like a mess, but doable. I would only start with the scripts that are necessary.

I don't know which ones are absolutely necessary. @kvg?

winni2k commented 2 years ago

I mean, i have used the mccortex conda package for years without any need for scripts. Why not create a separate conda package just for the scripts? It could depend on the package with the binary.

mbhall88 commented 2 years ago

My personal use case was that I wanted to use the make-pipeline.pl script inside the biocontainer image that is built from the bioconda package. In hindsight I could just download that script and use it inside a conda env with mccortex installed... Maybe that is a better way of doing it rather than creating a new recipe?

winni2k commented 2 years ago

I think you should be just fine composing conda packages with the mccortex cons package. That package is just a binary if i recall correctly.