Code

Condaify all the tools#468

Code

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smondet merged 39 commits intomasterhammerlab/biokepi:masterfrom conda-allhammerlab/biokepi:conda-allCopy head branch name to clipboardAug 22, 2017

+860-280

Commits

Commits on Jun 2, 2017

• add support for installing bioconda tools

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• biocondaify: OptiType

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• add support for transforming fastq_reads and re-use metadata

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• biocondaify: seqtk

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• fetch tool name and versions from the machine defaults

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• biocondaify: seq2HLA

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• improve the way we handle HLA files/tools

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• biocondify and upgrade picard

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• add snpeff-based annotation support

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• name HLA/VCF extraction nodes after the original ones

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• Allow tool-specific variables to be used in conditional checks

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• allow overriding shell when asking for the host

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• create bwa-mem-based optitype's workdir before attempting to write there

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• make use of the new shell override function

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• also mkdir for the new fastqs

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• fix path issues with optitype index

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Commits on Jun 3, 2017

• add forgotten optitype init to prepend the filtering

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Commits on Jun 8, 2017

• wip: cnvkit

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• init optitype

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• partially commented out code so that it can compile

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Commits on Jun 9, 2017

• minor style fix to the conda env

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• isolate bwa and optitype work folders better and initialize optitype when needed

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• wip: cibersort

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Commits on Jun 10, 2017

• wrap mutect with a java-7 conda environment for compatibility

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• comment out cibersort for now

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• bump vaxrank

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Commits on Jun 17, 2017

• just a bit more ciber

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Commits on Jun 30, 2017

• wip: cibersort

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Commits on Jul 10, 2017

• save vaxrank's debug output together with the reports

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Commits on Jul 11, 2017

• bump vaxrank version

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Commits on Jul 12, 2017

• use '.' instead 'source' for better shell compatibility

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• add base_packages to the python tool definitions

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Commits on Jul 17, 2017

• fix Strelka's subfolder mod for convenience

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Commits on Aug 17, 2017

• Merge master into conda-all

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Commits on Aug 18, 2017

• Fix naming in type python_version_type

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Commits on Aug 21, 2017

• Fix Strelka's installation

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• Fix Vaxrank.move_vaxrank_product

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• Remove commented-out/obsolete Cibersort code

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• Remove commented-out/obsolete CnvKit code

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