Open Kincekara opened 1 month ago
I dare to update this tool and I regret it. pip installation fails because of legacy libraries. mamba image became too big. So, I ended up using setup.py.
We thank you for your efforts 👏
It looks like there are some built-in tests that test a few different components. Could you try adding these test commands somewhere in the test stage and see what happens? see here: https://github.com/phac-nml/sistr_cmd?tab=readme-ov-file#development
@kapsakcj I tried to run internal tests via pytest but got errors mostly related to files. I am not sure that those tests are completed or compatible with this version. Instead, I added the test fasta as another test. By the way, version 1.1.3 is coming. We can wait a little more...
Darn OK. Thanks for trying anyways. Glad you added the additional test and thanks for making my requested changes.
I'm fine if you want to wait for v1.1.3, whatever you think is best. I don't think the changes between 1.1.2 and 1.1.3 look too drastic, but may be important for anyone working on serovars that are going to be updated in 1.1.3: https://github.com/phac-nml/sistr_cmd/blob/v1.1.3/CHANGELOG.md
There is something sketchy in the results. I am leaving this as a draft for now. I will do some more tests when I have time. In the meantime, if it is updated I'll change the version too.
Closes #1001 I dare to update this tool and I regret it. pip installation fails because of legacy libraries. mamba image became too big. So, I ended up using setup.py. I added a readme file and a test. It looks like it is working but it may be good to test it further.
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
)