Dr. K. D. Murray

I've recently taken on co-maintaining `bash_kernel`, and I'm currently closing all old/stale issues. I'm closing this issue as it should have been solved in version 0.8 with PR #120. Please...

This ties in very closely with the work I will be doing with @mr-c, a brief overview of which is in the wiki at [Userspace Container Review](https://github.com/common-workflow-language/common-workflow-language/wiki/Userspace-Container-Review).

> > Do I understand correctly nothing really forces to spawn bash process the moment kernel starts? Could wait to receive first code cell, which could contain %magic config statements....

Impressive, but without meaning any offence, this definitely falls in the category of >" But every idea I've seen so far is really janky - not just to implement, but...

This has something to do with conda's PS1 hackery. It can be worked around by setting `changeps1: false` in `~/.condarc`, or `conda config --set changeps1 false`. I *think* there's no...

I've seen this occasionally when a previous cell was either incomplete[0] or was swallowing stdin[1]. When this next occurs, please try restarting the kernel, and if the problem persists then...

implemented by @janpfeifer in #122

After about 2012 (Illumina 1.8+) illumina uses sanger quality encoding, so as counter-intuitive as it seems you probably want `-t sanger`. See the rather brilliant wiki page for more info:...

I'm working on an implementation of this, I'll give you a branch to test later this week @MaximilianStammnitz

Hello @Abieskawa, It looks like Sphinx, which I use to build the documentation, is broken on your system. I have no Mac system on which I can test why, so...