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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-06-04 12:55:28 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-06-04 12:57:08 +0200 |
| commit | d06ae0580848f9fafdbd4337aef58f80b537d662 (patch) | |
| tree | 717481b890867d9a82e78c052c84e1d98638fa04 | |
| parent | 4f773bc22df4aebd340f1a4a7d05d357351925a1 (diff) | |
| download | guix-d06ae0580848f9fafdbd4337aef58f80b537d662.tar guix-d06ae0580848f9fafdbd4337aef58f80b537d662.tar.gz | |
gnu: Add pigx-sars-cov2-ww.
* gnu/packages/bioinformatics.scm (pigx-sars-cov2-ww): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 48 |
1 files changed, 48 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 408c93bd34..6cfe82fc90 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") |