scholtalbers

Fix/slurm out of memory warning exit code 0:125

5

We receive these warning messages (OUT_OF_MEMORY but with exit code 0:125) a lot on our cluster and the jobs are to be considered successful https://bugs.schedmd.com/show_bug.cgi?id=3820#c62

[WIP] add an 'api' endpoint /api/docs/ to display all(?) available api urls…

4

After the idea of the DRF browsable API, this would add an 'api' endpoint `/api/docs/` to display all(?) available api urls/methods and their docstring. Currently this would look like below...

WIP: adding the docker container for an openldap server

2

XREF: https://github.com/scholtalbers/docker-galaxy-openldap/issues/1 I started this branch a while ago but couldn't actually get the `./buildlocal.sh` working at the time, so this is the state I left it at (did do...

replace <> by != for python3 galaxy instance

2

Untested but I believe this correctly updates some wrappers to work on a python3 hosted Galaxy instance. Seems also some autoformatting/whitespace removal happened - could remove that if need be.

feature request: eb create_easyconfig_from_pypi

1

Multiple times I have started writing an easyblock and in the end gave up and went the easy way to conda install stuff for users. This is mainly because of...

This might also be missing from the Galaxy instance, but it would be really helpful to be able to delete user visualizations through the API/Bioblend.

planemo serve - automatically upload test-data

2

Note: It may well be that I just don't find the right argument? It would be nice for `planemo serve` to automatically upload the files in `test-data` to the current...

I would like to keep control of how my local data, particular the genome references, appear in all tools and the `` gets in the way. Could it just be...

Sam_to_bam - make reference genome selection optional

1

Most SAM files will have the header and so samtools does not need the reference, therefor the reference genome selection could or should be optional.

How to use UPath and fsspec for file operations on multiple backends?

2

Not sure if this is the right place to ask this question, and I debated if it should go in the [community Q&A](https://github.com/fsspec/community/discussions)? Anyway, I want to leverage UPath and...