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Guix packages

To deploy GN we have packages in Guix itself (that comes with a distribution), in guix-bioinformatics and in guix-past (for older packages).

Typically run a guix pull to get the latest guix:

mkdir -p ~/opt
guix package -i guix -p ~/opt/guix

and checkout guix-past and guix-bioinformatics using git.

Now Guix should be happy with

~/opt/guix-pull/bin/guix package -L ~/guix-bioinformatics/ -L ~/guix-past/modules/ -A genenetwork
genenetwork1            0.0.0-2.acf65ac out     /home/wrk/guix-bioinformatics/gn/past/genenetwork1.scm:148:4
genenetwork2            3.11-2.1328932  out     /home/wrk/guix-bioinformatics/gn/packages/genenetwork.scm:452:4
genenetwork3            0.1.0-2.e781996 out     /home/wrk/guix-bioinformatics/gn/packages/genenetwork.scm:107:4

and we can try building

~/opt/guix-pull/bin/guix build -L ~/guix-bioinformatics/ -L ~/guix-past/modules/ genenetwork2

Any errors at either command means that we have to fix packages.

Note that you can use tux02 as a substitute server, see the README in guix-bioinformatics. That means that any package you build on tux02 can be downloaded from guix.genenetwork.org. So, best to build on tux02 - so everyone can share!

On tux02, to ramp up parallel building speed, you may want to use `-c 24 -M 24 -k` switches.

Fixing a package

Here python-pingouin failed. Which is pulled in by

tux02:~/guix-bioinformatics$ grep -r pingouin *
gn/packages/genenetwork.scm:             python-pingouin

git blame shows it was added in summer by Arun as part of the genenetwork3 package. A check of genenetwork3 shows

tux02:~/genenetwork3$ git blame gn3/computations/correlations.py

it was added by Alex in 2021.

Now it is not puzzling why the tests fail for this package as the Guix package does not build on the build farm, see

I am going to disable it for testing. By introducing the override

(define python-pingouin-without-tests
   (inherit python-pingouin)
    (substitute-keyword-arguments (package-arguments python-pingouin)
      ((#:tests? _ #f) #f)))))
(made with skribilo)