John Eppley

> One issue that I could see in many instances when executing the code: > `No kaiju DB found in /media/sfodata/databases/kaiju/nr_euk. Skipping Kaiju No kaiju DB found in /media/sfodata/databases/kaiju/nr_euk. Skipping...

No, I'm sorry. If I recall correctly, we do not extract the DTR sequence. The pipeline just runs minimap2 and inspects the PAF output (which does not include sequences, only...

I won't have time to check into this until later, but our pipeline was built and tested on python 3.7. Python 3.8 arrived in bioconda this month. Try changing "python...

I've looked into this a little more. First, my suggestion above was not 100% correct. That will get you python 3.7.0. To get the latest python 3.7 the environment.yml file...

Snakemake is trying to build dedicated conda environments for some of the workflow steps. These are defined in the `envs/*.yml` files. You can adjust the version requirements in those. What...

> Any progress here? Since the last mention of discussions with Amazon it's been 6 months. > > Maybe some other infrastructure may have become free to use in the...

I would like this, too. There are some tools I need to use that don't have a conda package but conflict with snakemake (usually because they want python 2). Snakemake...

I still see some use cases for named environments. #### 1. same workflow run in multiple places * This is just a performance concern, but it's wasteful of disks, processors,...

@johanneskoester, thanks for listening, and thank you for making such an incredibly useful piece of software.

That did the trick for me. Thanks.