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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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CI tests with Debian? #98

Open smoe opened 3 years ago

smoe commented 3 years ago

I do not really dare to ask, knowing how much you are investing into guix, but on the other hand, for the same reason you can also well estimate how much an effort it is to maintain the same packages with Debian. pigx-rnaseq is special to Debian, since it is the first RNA-seq pipeline that is fully packaged.

Would you think it to beneficial for pigx-rnaseq to have itself autobuilt with debian:latest upon commits with the help of travis? Dependencies are listed here and how to build it - well, who knows this better than you.

You are certainly aware of https://travis-ci.org/ (their offices are an extended lunchbreak away from yours) and to install dependencies is not much more than a copy'n'paste from the debian/control file referenced above. Maybe you also find a way to perform a dual testing of Debian- and guix-derived workflows, so we can find notable differences early. Be it for one of the R packages or one of the executables, knowing about differences should well help with the hardening of pigx-rnaseq, I tend to think.

rekado commented 3 years ago

I wouldn't mind adding a travis task to build pigx-rnaseq with Debian, but I'm not motivated to do the work :)

We're already building pigx-rnaseq automatically with Guix (albeit not on each commit), see e.g. https://ci.guix.gnu.org/build/595575/details

smoe commented 3 years ago

That is good. I think I can help with the setup of travis if that is the work that you are concerned about. What is important to me is that you are CIing on Debian unstable, not on Debian stable, since this to which we upload the new package and hence we can have the quickest turn around.

The guix package of Debian, on a sidenote, works very well. And I already have installed pigx-rnaseq with it. So, with every commit, it would be fairly easy to compare the two results. Just tell me.