feat: add docker container for vcf2cytosure

[ashwini06]

This PR:

Previously vcf2cytosure is added to the annotate container in PR #650. But there exists a problem loading vcf2cytosure in this container

The problem might be with the loading entry points for vcf2cytosure installation and its installation exited..

Removed: vcf2cytosure from annotate container

Added: New Docker container for vcf2cytosure. Related to #858

Review and tests:

• Tests pass
• Code review
• New code is executed and covered by tests, and test approve

[codecov]

Codecov Report

Merging #869 (0c6ee47) into develop (8c2b2af) will decrease coverage by 0.05%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop     #869      +/-   ##
===========================================
- Coverage    99.65%   99.60%   -0.06%     
===========================================
  Files           29       29              
  Lines         1761     1761              
===========================================
- Hits          1755     1754       -1     
- Misses           6        7       +1     

Flag	Coverage Δ
unittests	99.60% <ø> (-0.06%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
BALSAMIC/constants/common.py	100.00% <ø> (ø)
BALSAMIC/utils/cli.py	99.71% <0.00%> (-0.29%)	⬇️

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[ashwini06]

Tested the new container. vcf2cytosure is installed correctly

Also noted that the current container tests for annotate (same code in all container tests) didn't really capture the problem with loading vcf2cytosure
The code in the container tests https://github.com/Clinical-Genomics/BALSAMIC/blob/70fbdbe718edcd42e165442a521444fcb41d5c55/container_tests/annotate/annotate.sh#L8 only check fo the path but doesn't look for loading of the tool for eg: vcf2cytosure --help (error like in description screenshot) is not actually captured.

Coverage is dropped, because of this https://app.codecov.io/gh/Clinical-Genomics/BALSAMIC/compare/869/changes#D1L490. By simply removing these pip installation of bioinfo-tool will solve the coverage drop, but I would like to leave it as such, so we have an open option for installing bioinfo-tools via pip in the container in the future.

Regarding this https://github.com/Clinical-Genomics/BALSAMIC/pull/869/checks?check_run_id=5393027413, I tried the option with pip install --no-cache-dir . but that has problems with vcf2cytosure installation with constants module.
@ivadym let me know if you have any suggestions on this part.

[ivadym]

👍

Regarding your comment, it seems that Python does not know where to look for the required modules, but it should be solved setting explicitly the PYTHONPATH environment variable. I tested it locally with the changes that I suggested and it works:

[ashwini06]

👍

Regarding your comment, it seems that Python does not know where to look for the required modules, but it should be solved setting explicitly the PYTHONPATH environment variable. I tested it locally with the changes that I suggested and it works:

Thanks @ivadym for your suggestions :) It works fine now with your suggestions

[sonarqubecloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[ashwini06]

@ivadym @khurrammaqbool : Ready for review 🔈

[ivadym]

👍