one Conda environment to rule them all

[maxulysse]

• Remove GetVersionAlleleCount and GetVersionASCAT processes
• Remove r-base and runallelecount containers
• Install cancertit-allelecount 2.1.2 with Bioconda
• Install RColorBrewer 1.1 with Conda
• Install Bioconductor-Rtracklayer 1.42.1 with Bioconda
• Update BCFTools from 1.8 to 1.9
• Update GATK4 from 4.0.9.0 to 4.1.0.0
• Update Manta from 1.4.0 to 1.5.0
• Update samtools from 1.8 to 1.9
• Update Strelka from 2.9.3 to 2.9.10
• Update VCFanno from 0.3.0 to 0.3.1
• Update VEP cache from 95 to 96
• Update VEP version from 95.2 to 96.0

PR checklist

• [X] PR is made against dev branch
• [X] This comment contains a description of changes (with reason)
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [X] Ensure the test suite passes (./scripts/test.sh -p docker -t ALL).
• [X] Documentation in docs is updated
• [ ] CHANGELOG.md is updated

[maxulysse]

Obviously failing because VEP is requesting cache and software version 96, and the container is currently only in 95. Need to update at least allelecount in bioconda before continuing on that updating of all tools.

[apeltzer]

Started working on alleleCount: https://github.com/bioconda/bioconda-recipes/pull/14740

[maxulysse]

Thanks, I tried doing it, but I'm definitively not as efficient. Can you add 2.2.0 as well, so that we can start with the same version we're currently using?

[apeltzer]

cancerit-allelecount=4.0.2 is now on bioconda. https://anaconda.org/bioconda/cancerit-allelecount/files