The source repo has moved to

• https://git.genenetwork.org/genecup/

If you have ssh access you can push to the repo with

• yourname@git.genenetwork.org:/home/git/public/genecup

On Tux02 as shepherd user I can build:

./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8

To run genecup in a container we have a trick to include the source code by cd'ing into the built version

export EDIRECT_PUBMED_MASTER=/export2/PubMed
export TMPDIR=/export/ratspub/tmp
export NLTK_DATA=/export2/PubMed/nltk_data

# This version for the genecup guix profile which includes guix-bioinformatics, using genecup-channels.scm.
# shepherd@tux02:~/services/genecup$ ./guix/bin/guix build -L ~/services/genecup/guix-past/modules -L ~/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 24 -M 8

cd /home/shepherd/services/genecup
cd $(/home/shepherd/services/genecup/guix/bin/guix build -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native -c 4)

/home/shepherd/services/genecup/guix/bin/guix shell -C -N --expose=/etc/ssl/certs --expose=$EDIRECT_PUBMED_MASTER --share=$TMPDIR -L /home/shepherd/services/genecup/guix-past/modules -L /home/shepherd/services/genecup/guix-bioinformatics genecup-latest-with-tensorflow-native coreutils-minimal -- env TMPDIR=$TMPDIR EDIRECT_PUBMED_MASTER=$EDIRECT_PUBMED_MASTER NLTK_DATA=$NLTK_DATA ./server.py

That means you can also develop software running in a container with the last command by switching into a repo:

cd $repo
run last command using guix shell

The only problem, at this point, is that python is not in the path.

The alternative is to use a guix shell, as described in the README.md

• https://git.genenetwork.org/genecup/tree/README.md

and port forward:

ssh -L 4200:127.0.0.1:4200 -f -N server
curl localhost:4200