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branch master updated: gnu: Add pigx-sars-cov2-ww.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add pigx-sars-cov2-ww. |
Date: |
Fri, 04 Jun 2021 06:59:19 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new d06ae05 gnu: Add pigx-sars-cov2-ww.
d06ae05 is described below
commit d06ae0580848f9fafdbd4337aef58f80b537d662
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Jun 4 12:55:28 2021 +0200
gnu: Add pigx-sars-cov2-ww.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
---
gnu/packages/bioinformatics.scm | 48 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 48 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 408c93b..6cfe82f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10633,6 +10633,54 @@ and interactive quality reports. The pipeline is
designed to work with UMI
based methods.")
(license license:gpl3+)))
+(define-public pigx-sars-cov2-ww
+ (package
+ (name "pigx-sars-cov2-ww")
+ (version "0.0.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
"https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/"
+ "releases/download/v" version
+ "/pigx_sars-cov2-ww-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1h1rfl3dyf7pid74xxgiyr4x1l5yj000wcz5crm1bdbaz8p7b7ic"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("bash-minimal" ,bash-minimal)
+ ("bwa" ,bwa)
+ ("ensembl-vep" ,ensembl-vep)
+ ("fastqc" ,fastqc)
+ ("kraken2" ,kraken2)
+ ("krona-tools" ,krona-tools)
+ ("lofreq" ,lofreq)
+ ("multiqc" ,multiqc)
+ ("prinseq" ,prinseq)
+ ("python-pyyaml" ,python-pyyaml)
+ ("python-wrapper" ,python-wrapper)
+ ("r-base64url" ,r-base64url)
+ ("r-dplyr" ,r-dplyr)
+ ("r-dt" ,r-dt)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-magrittr" ,r-magrittr)
+ ("r-minimal" ,r-minimal)
+ ("r-plotly" ,r-plotly)
+ ("r-qpcr" ,r-qpcr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-stringr" ,r-stringr)
+ ("r-tidyr" ,r-tidyr)
+ ("samtools" ,samtools)
+ ("snakemake" ,snakemake)))
+ (home-page "https://bioinformatics.mdc-berlin.de/pigx/")
+ (synopsis "Analysis pipeline for wastewater sequencing")
+ (description "PiGx SARS-CoV-2 is a pipeline for analysing data from
+sequenced wastewater samples and identifying given variants-of-concern of
+SARS-CoV-2. The pipeline can be used for continuous sampling. The output
+report will provide an intuitive visual overview about the development of
+variant abundance over time and location.")
+ (license license:gpl3+)))
+
(define-public pigx
(package
(name "pigx")
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