Sarah Nadeau

I'd love to tackle this for some images but I will need to re-work my approach. In my fork I was pushing test data through a whole sequence of tools,...

In case anyone else runs into this, I got the same error and I think I it comes from swga looking for dsk in the wrong place. https://github.com/eclarke/swga/blob/b36cefaeb50d595e34068a86f466c3c9fde5aab7/swga/utils.py#L63 I have...

Same thing applies for set_finder from cliquer, which is needed for `swga find_sets`: ``` cp /usr/local/bin/set_finder /usr/bin/set_finder ```

Thanks for the speedy reply! Actually, both versions were built from source. I noticed the same thing when I use the same Dockerfile to build from source as part of...

In case it helps, here's an example of the different SNP alignments from ParSNP built using the same Dockerfile on my laptop vs in the GitHub actions workflow and the...

Sorry about that, I renamed the script in the meantime. Here's the new link and I've also attached it as a zip archive. [https://github.com/SarahNadeau/bioinf-containers/blob/master/parsnp/tests/scripts/run_positive_control.sh](https://github.com/SarahNadeau/bioinf-containers/blob/master/parsnp/tests/scripts/run_positive_control.sh) [run_positive_control.sh.zip](https://github.com/marbl/parsnp/files/7727534/run_positive_control.sh.zip)

Hi @bkille I just wanted to follow up that I am having the same issue with ParSNP when installed via conda in a Docker image. I've tried to make the...