updating freyja to 1.5.2 #1082
updating freyja to 1.5.2 #1082
Conversation
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@erinyoung When I check conda requirements, some of the libraries seem missing: pytest, flake8, coveralls, and scipy. I am not sure if those are for the tests or the program itself. Could you check them again? Please have mercy on my eyes and try not to use verbose (-vv) in pip installations. I can't follow the pip logs 👁️ 👁️ |
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pytest, flake8, coveralls, and scipy aren't in the bioconda recipe for 1.5.1 at https://bioconda.github.io/recipes/freyja/README.html and they aren't listed in their most-recent freyja PR into bioconda at https://github.com/bioconda/bioconda-recipes/pull/51511/files |
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@Kincekara , I removed the |
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Thank you for checking again. I believe those extra libraries are for the pytest. I have no further suggestions. The tests look good. I am merging and deploying this... |
There's a new version of Freyja!
1.5.2 was released last week, but it's stuck on bioconda - which is what 1.5.1 and prior dockerfiles use for installation with micromamba.
I copied the files from 1.5.1 and made several modifications. The original goal was to install freyja from source. Freyja has some common dependencies of samtools, ivar, and epiweeks which are fairly simple to install. I, however, have not been able to install usher from source (see #1014) , so I kept the base image as micromamba and then copied over the dependencies listed in the bioconda recipe and had all of those installed via micromamba.
Freyja is then downloaded with wget and installed via pip. Freyja's setup.py doesn't list all the python dependencies, so all the python dependencies (that I can find) are installed via micromamba.
Git is installed via apt-get because it is required when pip installs freyja.
I have also changed the github actions to update the workflow weekly instead of monthly, because I've been getting feedback that monthly just isn't often enough.
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)