add sciclone and cn.mops

[gatoravi]

cn.mops and sciclone are now used in clinseq. These are both R packages which need to be installed on the sgms. It looks like all our R packages are installed using the 'renv' method described here. It's currently unclear how to add new R packages using this method.

[malachig]

Hey @mcallaway, do you remember how this R package gets built. It seems like we just install one package renv and it dependencies we getting a working R install that is the correct version, is configured properly, has all the linux system dependencies we need (Cairo, etc.) and also has all of the R and Bioconductor libraries we need installed within it. How does all of this magic happen?

Are the R & Bioconductor packages somehow build into the renv package you created (2.15.3-1precise1~20140313)? If we want to add some new R libraries how would we do that?

Here are the package details for renv on a current test instance of the sGMS

sudo apt-cache policy renv
renv:
  Installed: 2.15.3-1precise1~20140313
  Candidate: 2.15.3-1precise1~20140313
  Version table:
 *** 2.15.3-1precise1~20140313 0
       1002 file:/opt/gms/4YDBW36/sw/apt-mirror-min-ubuntu-12.04-2015.03.30/mirror/repo.gsc.wustl.edu/ubuntu/ precise-genome-development/main amd64 Packages
        100 /var/lib/dpkg/status

[gatoravi]

The packages in lucid, here, that we need in precise currently are,

r-tgi-sciclone (>= 1.0.7-2)
r-bioc-cn.mops (= 1.8.9-1)

[gatoravi]

The goal here is to have a separate repo on github for the renv method or document clearly how this works and how to add/remove packages in the future.

[mcallaway]

I am making progress on the process for building the "renv" package, which will contain R 2.15.3 and our list of R packages. I'm noting a discrepancy in the list we have in genome-snapshot-deps-r.depends and the list I have in the "renv" package. I'm going to assume the r.depends list is more correct, update renv, and show you the results to see if we can come to agreement on what should be in our R environment.

Note that my "renv" package is built from a fresh virtual machine, provisioned with puppet. When I'm done, you'll be able to provision the VM yourself to make updates to the renv package.

I'm making fast progress. Hoping to have something done in a day or so.

[gatoravi]

@mcallaway has some awesome documentation on our internal page - here The procedure outlined there has to be tested out the next time we add/remove an R package to the SGMS. This resource could be helpful to folks outside TGI as well.

The new version of renv is now installed as expected from the new APT dump added here -https://github.com/genome/gms/commit/1d1d9ec3b0c23a23175d3062eb5e5d6f2313b953,

gmsuser@clia1 /opt/gms/IX7TW51/sw/workflow/lib/Workflow/DataSource (gms-pub-2015.02.22)> apt-cache policy renv
renv:
  Installed: 2.15.3-1precise1~20150406
  Candidate: 2.15.3-1precise1~20150406
  Version table:
 *** 2.15.3-1precise1~20150406 0
       1002 file:/opt/gms/IX7TW51/sw/apt-mirror-min-ubuntu-12.04-2015.04.09/mirror/repo.gsc.wustl.edu/ubuntu/ precise-genome-development/main amd64 Packages
        100 /var/lib/dpkg/status

Sciclone and CnMops are succesfully installed.