Nate Coraor

`SHA*_Init()`, `SHA*_Update()` and `SHA*_Final()` are deprecated in OpenSSL 3 (which ships in EL9) and are replaced by `EVP_DigestInit_ex()`, `EVP_DigestUpdate()`, and `EVP_DigestFinal()`. Although the old functions are still usable, if you...

This is mainly useful to me for the job destination parameters case I added to the `aq` help text.

[24.2] Add option to disable auto_install in cached_explicit_singularity

9

Without this option there's no way to prevent writing to the cache and falling through to other resolvers if the image is not there. This will allow preconverting explicit docker...

Automatically initialize Apptainer

1

Ultimately the goal here is to support easier production deployments where Galaxy itself does not have to be installed in the shared FS. Admins can configure the `tool_dependency_dir` to be...

In MultiQC, the inputs are symlinked based on the name and [a conflict check](https://github.com/galaxyproject/tools-iuc/blob/a9d3251b40bc6ae1147b2e013d623f957a981421/tools/multiqc/macros.xml#L54-L57) is done to add an incrementing number to the name if multiple names collide. However, the...

Update HISAT2 DM for normalized layout, plus other fixes:

1

- Drop python wrapper - Update HISAT2 version - Add test of (some) non-default options I apparently missed this one in #6489. Other stuff: - Fix data table entry for...

Bowtie2 DM puts the wrong path in the loc file

1

The latest update to the DM (by me) caused the path to be to the sequence .fa file, but it should be to the sequence id. Currently: ``` /data/hg38/bowtie_index/v2/hg38/hg38.fa ```...

stdout/stderr truncation removes the significant part

3

We truncate the stdout/stderr stored in the database at 32 KB, so this means that the end is lost. If there's a problem, the end is probably far more relevant...

The Google Drive file source template uses the `drive.file` permission which means that Galaxy can only access Drive contents that the user has created with Galaxy (and specifically, that Galaxy...

Delegate group membership administration to non-admins

4

This would be super useful for e.g. groups used only for library access. Currently only admins can modify group membership. The caveat is that anyone delegated this permission would have...