adds sistr 1.1.2

[Kincekara]

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:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[kapsakcj]

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

[Kincekara]

@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...

[kapsakcj]

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

[Kincekara]

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.

[Kincekara]

I realized the previous image base is xenial. When I used focal instead of jammy, all pip problems were resolved. This way looks cleaner, so I decided to stick focal for now.

[kapsakcj]

FYI sistr 1.1.3 was just released https://github.com/phac-nml/sistr_cmd/releases/tag/v1.1.3

[Kincekara]

😭 😭 😭

[erinyoung]

I just got to this PR today. I think it looks good to merge and deploy and 1.1.3 can come later.

[Kincekara]

Agreed! I am merging this one while it is still working. I will open an issue for 1.1.3