use mip-rna rna upload for tomte

[rannick]

Description

Implementing scout changes from Clinical-Genomics/scout#4799.
Tomte RNA cases will be loaded to existing RNA cases similarly to MIP-RNA cases, with the addition of omics files (fraser and outrider), an option to load the rna_genome_build, a command to link the sample internal id to the dna/rna cases as fraser and outrider have this id in their output and a command to load the variant outlier

Added

• Loading omics files, rna_genome_build, variant outlier to scout for tomte analyses

Changed

• Move get_genome_build into utils

Fixed

• Use tags instead of hard-coded string for scout tags in upload

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_cg -t cg -b [THIS-BRANCH-NAME] -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[Vince-janv]

Great work! ⭐ Thanks for your patience ⏳

[rannick]

And thank you for yours!

[rannick]

Building wheels for collected packages: cg
  Building wheel for cg (pyproject.toml) ... done
  Created wheel for cg: filename=cg-63.2.14-py3-none-any.whl size=7645883 sha256=5edb8c46733d0c249c846c65ba5a59752cf0fa06cf48c67d734cc260515df661
  Stored in directory: /tmp/pip-ephem-wheel-cache-ola8srjd/wheels/37/af/fb/bcc5d9ebea8d2d21eed83cc632a0fd452ff5f5a7f6239cfe6e
Successfully built cg
WARNING: Ignoring invalid distribution ~g (/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages)
Installing collected packages: cg
WARNING: Ignoring invalid distribution ~g (/home/proj/stage/bin/miniconda3/envs/S_cg/lib/python3.11/site-packages)
Successfully installed cg
fatal: Not a git repository (or any parent up to mount point /home)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
repository is clean
Logging deploy ...
Getting deployer... done.
Getting last commit message and SHA... done.
Getting version of deploy scripts... /home/annick.renevey
done.
Log deploy... done.
cg, version 63.2.14