Streamline installation process

[messersc]

Hi,

the current installation is a little cumbersome and I think we can make it easier with little effort. The reason is that all the software that gets installed outside of conda right now if you follow the wiki page is also available through conda. In the end, of course it would be very nice if Clinker itself would also make to bioconda.

Short-term, we can aim for an environment.yaml file (https://conda.io/docs/user-guide/tasks/manage-environments.html#create-env-file-manually).

Note that the conda r channel is not needed anymore, if we use the multichannel defaults (conda/conda#7695 (comment))

For example:

name: clinker
channels:
  - defaults
  - bioconda
  - conda-forge
dependencies:
  - python=2.7
  - star=2.5.3a
  - samtools
  - bpipe
  - bioconductor-gviz # pulls biomart, R
  - libiconv

The above is untested, I'll let you know how it goes and then we can decide what the best course of action is.

Clemens

[breons]

Thanks, Clemens, this looks cool. The shareable environment is a good idea and would definitely make installation more simple.

Let me know how you go :).

[andrewlonsdale]

I actually submitted a Clinker recipe for bioconda a little while ago, but it missed a QC check at some point and there might be an issue with it. It's here: https://github.com/bioconda/bioconda-recipes/tree/fe678d1b7817c221e58888ccba98e4b52b733534/recipes/clinker

I'm hoping to revisit it or help with this effort, but either way, this would be great to get going

[messersc]

I see, I only checked the package search and not the recipes. But this is really strange, it was merged into master but apparently there is no package...

I added libiconv above, which was missing and I also had some problems with bioconductor-genomeinfodb and bioconductor-genomeinfodbdata, where apparently the conda packages did not work and I needed to install from bioconductor directly.

But first, we really need to find out why this package does not show up...