diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/systems/apps.gmi | 60 |
1 files changed, 55 insertions, 5 deletions
diff --git a/issues/systems/apps.gmi b/issues/systems/apps.gmi index 3ced6ab..9da5b72 100644 --- a/issues/systems/apps.gmi +++ b/issues/systems/apps.gmi @@ -10,19 +10,69 @@ GeneNetwork.org retains a number of apps. Currently they are managed by shepherd * priority: medium * keywords: system, sheepdog, shepherd +# Tasks + +* [ ] Get services running +* [ ] Move guix shell into containers +* [ ] Make sure the container starts up on reboot and/or migrate to a new host + # List of apps Current apps managed by shepherd on tux02 are -* [ ] genecup (hao) -* [ ] bnw (yan cui and rob) +* [+] genecup [shell] (hao) +* [X] bnw [container] (yan cui and rob) * [ ] genome-browser (defunct) * [ ] hrdp-project (hao?) -* [ ] pluto (saunak) +* [+] pluto (saunak) * [ ] power (dave) -* [ ] rn6app (?) * [ ] root? +* [+] Longevity explorer [container] (dave) * [ ] singlecell (dave) * [ ] jumpshiny app (xusheng) +* [+] hegp (pjotr) +* [-] rn6app (hao - remove) + +To fix them we need to validate the sheepdog monitor and make sure they are working in either shepherd (+), or as a system container (X). + +# Info + +## BNW + +The app is already a Guix system container! To make it part of the startup I had to move it away from shepherd (which runs in userland) and: + +``` +/home/shepherd/guix-profiles/bnw/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network +ln -s /gnu/store/0hnfb9ynnxsig3yyprwxmg5h6c9g8mry-run-container /usr/local/bin/bnw-app-container +``` + +systemd service: + +``` +root@tux02:/etc/systemd/system# cat bnw-app-container.service +[Unit] +Description = Run genenetwork BNW app container +[Service] +ExecStart = /usr/local/bin/bnw-app-container +[Install] +WantedBy = multi-user.target +``` + +We need to make sure the garbace collector does not destroy the container, add the --root switch + +``` +/home/shepherd/guix-profiles/bnw/bin/guix system container /home/shepherd/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/shepherd/logs/bnw-server=/var/log --network --root=/usr/local/bin/bnw-app-container +``` + +Check with + +``` +root@tux02:/home/shepherd# /home/shepherd/guix-profiles/bnw/bin/guix gc --list-roots |grep bnw + /usr/local/bin/bnw-app-container +``` + +## jumpshiny -To fix them we need to validate the sheepdog monitor and make sure they are working in either shepherd, or as a system container. +jgart@balg01:~/gn-machines$ guix system container --network -L . -L ../guix-bioinformatics/ -L ../guix-past/modules/ --substitute-urls='https: +//ci.guix.gnu.org https://bordeaux.guix.gnu.org https://cuirass.genenetwork.org' test-r-container.scm -L ../guix-forge/guix/ +/gnu/store/xyks73sf6pk78rvrwf45ik181v0zw8rx-run-container |