Add r-base as a dependency

[rhpvorderman]

r-base is needed for picard CollectMultipleMetrics, CollectInsertSizeMetrics etc. (basically anything with metrics).

• I have read the guidelines for bioconda recipes.
• This PR adds a new recipe.
• AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
• This PR updates an existing recipe.
• This PR does something else (explain below).

[bgruening]

#3859 :(

[rhpvorderman]

#3859 :(

@bgruening. I posted my opinion on the issue.

[rhpvorderman]

@bgruening , given that there was no great backlash on the issue, I think that nobody strongly cares about this. Shall we go ahead and merge this?

[bgruening]

@dpryan79 any opinion?

[dpryan79]

I’m a very weak “no” on this. Picard is just so bloated as is and I have to say this is the first time I’d heard that Picard did any plotting on this.

…

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On 2. Aug 2019, at 17:26, Björn Grüning ***@***.***> wrote: @dpryan79 any opinion? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[cbrueffer]

I tend to agree that things should work out of the box, although I have to admit I shared Devon's unawareness regarding the R dependency. Given the bloat having a picard-lite recipe and pointing to that in the picard install message would be good.

[biocondabot]

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
noarch	picard-2.20.4-1.tar.bz2	repodata.json
noarch	picard-slim-2.20.4-0.tar.bz2	repodata.json

---

You may also use conda to install these:

• For packages in noarch:

  conda install -c https://67568-42372094-gh.circle-artifacts.com/0/tmp/artifacts/packages <package name>
  

---

Docker image(s) built:

Package	Tag	Install with docker
picard-slim	2.20.4--0	show curl "https://67568-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/picard-slim%3A2.20.4--0.tar.gz" | gzip -dc | docker load
picard	2.20.4--1	show curl "https://67568-42372094-gh.circle-artifacts.com/0/tmp/artifacts/images/picard%3A2.20.4--1.tar.gz" | gzip -dc | docker load

[rhpvorderman]

@bgruening @dpryan79 @cbrueffer
The previous iteration of picard has been renamed to picard-slim.
While copying the package I found that a bash wrapper script is used to run picard instead of a python wrapper script. So I removed the python dependency in both picard and picard-slim.

Is this compromise to your liking?

EDIT: Also updated the branch with master.

[dpryan79]

👍 from me. @bgruening @cbrueffer thoughts?

[cbrueffer]

Looks good; a post-install message in each of the recipes pointing to the other one would be nice ("A package without the R dependency is available as picard-slim or similar); see e.g. recipes/braker2/post-link.sh.

[bgruening]

Fine with me ...

[rhpvorderman]

Looks good; a post-install message in each of the recipes pointing to the other one would be nice ("A package without the R dependency is available as picard-slim or similar); see e.g. recipes/braker2/post-link.sh.

@cbrueffer I do agree that users need to be notified. While working on the post-link script however, I felt that I had to write a really, really good message that would be worth it for the user to see every time they install picard. This is IMO not possible. It is a very annoying way to let users know.

I have added information about picard and picard-slim to the package descriptions, so that users can make an informed decision on which package to install based on the information on bioconda.github.io.

If these descriptions are okay I will merge the branch.

[cbrueffer]

Thanks @rhpvorderman , I like the idea.

[alanhoyle]

Can this be added to the gatk4 as a dependency as well?