# Apps

GeneNetwork.org retains a number of apps. Currently they are managed by shepherd as `guix shell` services, but we should really move them to system containers.

# Tags

* assigned: pjotrp
* type: enhancement
* status: in progress
* 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 [shell] (hao)
* [X] bnw [container] (yan cui and rob)
* [ ] genome-browser (defunct)
* [ ] hrdp-project (hao?)
* [+] pluto (saunak)
* [ ] power (dave)
* [ ] 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

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