Script availability in conda recipe
mbhall88 opened this issue · 6 comments
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?
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.
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...
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?
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.
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?
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.