Pablo Moreno

Startup time for galaxy web container can take very long

19

First, let me say how great this setup has become, you have done a fantastic job guys! On a more or less unmodified setup, I often observe that the galaxy...

Helm delete leaves some remanent behind

5

Doing: ``` $ helm list NAME NAMESPACE REVISION UPDATED STATUS CHART APP VERSION galaxy-dev default 54 2022-12-16 15:55:08.025324 +0000 UTC deployed galaxy-5.3.1 22.05 netdata default 1 2022-11-16 15:52:08.753301 +0000 UTC...

Database default space allowance gets filled fairly quickly

7

After only 10 executions or so of our single cell pipeline, the database disk got full: ``` root@galaxy-galaxy-dev-postgres-0:/home/postgres/pgdata# df -h . Filesystem Size Used Avail Use% Mounted on /dev/vdc 9.8G...

Run out of file locks after an hour of running (around ~100 jobs)

8

After around an hour of running I'm starting to get all sort of file locking errors in the main job handler: ``` galaxy.tool_util.deps.containers ERROR 2022-12-15 10:34:46,234 [pN:job_handler_0,p:8,tN:KubernetesRunner.work_thread-1] Could not get...

Galaxy workflow handler seems to have issues in communicating with Rabbit/AMPQ

3

For our setup, we normally install (and keep tools updated to new versions) through ephemeris shed-tools calls from a CI. It seems that the process of making all the different...

According to Marius' comments on https://github.com/galaxyproject/galaxy/issues/9483#issuecomment-634477538 (which also affects this setup), we need to add support for a better transport for kombu to avoid the described conflicts there.

Most of my usage in the past of Galaxy-k8s relied on tools being run as root, which is not ideal of course. In the current chart that is not longer...

Combination for update to scanpy tools IUC galaxy wrappers

2

This aims to add a new container for these minor set of changes in [tools-iuc/scanpy](https://github.com/galaxyproject/tools-iuc/pull/5206). It should specifically match these [new deps versions](https://github.com/galaxyproject/tools-iuc/blob/327881a8d914311de1ba43fd8171898e008dd0a8/tools/scanpy/macros.xml#L2-L11), which aim to mimic as much as...

For some reason, all the ebi-gxa/seurat_/3.1.1+galaxy depending on seurat-scripts 0.0.7 are not installed in the Human Cell Atlas flavour. They are not installed at all (they don't appear in the...

Should we make a bioconda package with the scripts in this repo?

2

Thanks for all the great things here, we reuse the same yaml structure for our own CI that installs our tools in our local instances. This includes having our own...