Add FreeBayes bamleftalign #391
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smondet
reviewed
Dec 9, 2016
| let reference_fasta = | ||
| Machine.get_reference_genome run_with reference_build | ||
| |> Reference_genome.fasta in | ||
| let name = sprintf "FreeBayes.bamleftalign %s" bam#product#path in |
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Maybe a Filename.basename would make the name more readable?
smondet
reviewed
Dec 9, 2016
| let freebayes = | ||
| Git_installable_tool.make | ||
| Machine.Tool.Default.freebayes | ||
| ~repository:"git://github.com/ekg/freebayes.git" |
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Maybe the https:// version is more portable (against firewalls & co).
| @@ -171,6 +171,11 @@ module type Bioinformatics_base = sig | |||
| [ `Bed ] repr -> | |||
| [ `Vcf ] repr | |||
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| val bam_left_align: | |||
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Here (in Semantics), I like adding doc-comments progressively for new tools.
| @@ -5,7 +5,7 @@ | |||
| FROM hammerlab/ketrew-server | |||
| # Installing easy Biokepi dependencies: | |||
| RUN sudo apt-get update | |||
| RUN sudo apt-get install --yes cmake r-base tcsh libx11-dev libfreetype6-dev pkg-config wget gawk graphviz xvfb | |||
| RUN sudo apt-get install --yes cmake r-base tcsh libx11-dev libfreetype6-dev pkg-config wget gawk graphviz xvfb git | |||
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Can you add the corresponding line in tools/docker/README.md?
|
@smondet back to you, thanks for the review! |
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fixes #390
(doesn't add the variant caller, to the workflow but all the infrastructure is there)