Edit this page | Blame

Troubleshooting inside the GN dev container

You need to find the development container so that you can begin troubleshooting:

ps -u root -f --forest | grep -A4 '/usr/local/bin/genenetwork-development-container' | grep shepherd

Example output:

root      16182  16162  0 03:57 ?        00:00:04  \_ /gnu/store/n87px1cazqkav83npg80ccp1n777j08s-guile-3.0.9/bin/guile --no-auto-compile /gnu/store/b4n5ax7l1ccia7sr123fqcjqi4vy03pv-shepherd-1.0.2/bin/shepherd --config /gnu/store/5ahb3745wlpa5mjsbk8j6frn78khvzzw-shepherd.conf

Get into the container:

# Use the correct pid and guix/bash path.

sudo /home/bonfacem/.config/guix/current/bin/guix container exec 16182 /gnu/store/m6c5hgqg569mbcjjbp8l8m7q82ascpdl-bash-5.1.16/bin/bash --init-file /home/bonfacem/.guix-profile/etc/profile --login

All the gn related logs can be found in "/var/log/cd":

genenetwork2.log
genenetwork3.log
gn-auth.log
gn-guile.log

All the nginx log are in "/var/log/nginx"

Sometimes, it's useful to trigger webhooks while troubleshooting. Here are all the relevant webhooks:

/gn-guile
/genenetwork2
/genenetwork3
/gn-libs
/gn-auth

Inside the container, we have "coreutils-minimal", and "curl" that you can use to troubleshoot.

(made with skribilo)