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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

https://packages.guix.gnu.org/packages/python-pingouin/0.5.2/

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

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