Tor Solli-Nowlan

I also have this issue on python3.9. If I upgrade mamba first and attempt to install the new conda version: ```` $ mamba --version mamba 0.24.0 conda 4.12.0 $ mamba...

it seems to update correctly now and function as expected :+1:

Singularity is affected by your local environment, so it can be a bit finicky. Try using `singularity exec --cleanenv ...`, it can solve a lot of mysterious / hard to...

Ah, I see now. You're calling the configfile, which the image tries to interpret using `/bin/sh`, rather than `AnnotSV`. Try with: ```shell singularity exec --cleanenv "$singularity_container" AnnotSV \ -SVinputFile "$file"...

> This could be ported to docker-machine, if the project finds a new life somewhere else ? > Like moby-machine and boot2moby, or whatever. Something that is accepting patches... Gitlab...

Ah, yeah. I suppose that while those could fix some issues they aren't really bug fixes themselves. It's pretty frustrating. Gitlab just had a docker-machine release a week ago, after...

We solve for this (also hackily) by using `multiqc -i $sample_id ...` and then filtering via `config_title` meta variable. Would definitely like to see a nicer solution, as the workaround...

I think it's useful as feedback on the filter, but not required for the 1.0. A new issue can be made for that though, since that's adding functionality to the...

For anyone else running into this issue, patched version available via: ```shell pip install PyVCF@git+https://github.com/ousamg/[email protected] ```

Not sure there's anyone around who can. Nothing has been merged in years, but I figured I'd create the PR just in case. Some alternatives: - Use the fork linked...