diff --git a/guix.scm b/guix.scm index c273817..7889da7 100644 --- a/guix.scm +++ b/guix.scm @@ -1,5 +1,5 @@ ;;; PiGx_bsseq - reports pipeline for reads from bisulfite experiments. -;;; Copyright © 2017, 2018 Ricardo Wurmus +;;; Copyright © 2017, 2018, 2020 Ricardo Wurmus ;;; ;;; This file is part of PiGx_bsseq. ;;; @@ -15,96 +15,19 @@ ;;; $ guix package --with-source=pigx_bsseq-0.0.1.tar.gz -f guix.scm ;;; ;;; This environment file was developed for Guix version -;;; v0.14.0-3177-gbcddf30af +;;; 1614862 -(use-modules (guix packages) - (guix licenses) - (guix download) - (guix build-system gnu) - (gnu packages) - (gnu packages autotools) - (gnu packages base) - (gnu packages statistics) - (gnu packages bioinformatics) - (gnu packages compression) - (gnu packages cran) - (gnu packages curl) - (gnu packages haskell) - (gnu packages java) - (gnu packages ncurses) - (gnu packages perl) - (gnu packages pkg-config) - (gnu packages python) - (gnu packages tls) - (gnu packages web)) +(use-modules (guix packages) (gnu packages)) (define %pigx-bsseq-version (symbol->string (with-input-from-file "VERSION" read))) -(define-public pigx-bsseq - (package - (name "pigx_bsseq") +(define-public pigx-bsseq-development + (package (inherit (specification->package "pigx-bsseq")) (version %pigx-bsseq-version) (source (string-append (getcwd) "/pigx_bsseq-" version ".tar.gz")) - (build-system gnu-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'set-timezone - ;; The readr package is picky about timezones. - (lambda* (#:key inputs #:allow-other-keys) - (setenv "TZ" "UTC+1") - (setenv "TZDIR" - (string-append (assoc-ref inputs "tzdata") - "/share/zoneinfo")) - #t)) - (add-after 'install 'wrap-executable - ;; Make sure the executable finds all R modules. - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (wrap-program (string-append out "/bin/pigx-bsseq") - `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))) - `("PYTHONPATH" ":" = (,(getenv "PYTHONPATH"))))) - #t))))) (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ("tzdata" ,tzdata))) - (inputs - `(("coreutils" ,coreutils) - ("sed" ,sed) - ("grep" ,grep) - ("r-minimal" ,r-minimal) - ("r-annotationhub" ,r-annotationhub) - ("r-dt" ,r-dt) - ("r-genomation" ,r-genomation) - ("r-methylkit" ,r-methylkit) - ("r-rtracklayer" ,r-rtracklayer) - ("r-rmarkdown" ,r-rmarkdown) - ("r-ggplot2" ,r-ggplot2) - ("r-ggbio" ,r-ggbio) - ("r-ggrepel" ,r-ggrepel) - ("r-reshape2" ,r-reshape2) - ("r-matrixstats" ,r-matrixstats) - ("r-data-table" ,r-data-table) - ("ghc-pandoc" ,ghc-pandoc-1) - ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) - ("python-wrapper" ,python-wrapper) - ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) - ("bismark" ,bismark) - ("fastqc" ,fastqc) - ("multiqc" ,multiqc) - ("bowtie" ,bowtie) - ("trim-galore" ,trim-galore) - ("cutadapt" ,cutadapt) - ("samtools" ,samtools))) - (home-page "https://github.com/BIMSBbioinfo/pigx_bsseq/") - (synopsis "Bisulfite sequencing pipeline from fastq to methylation reports") - (description "PiGx BSseq is a data processing pipeline for raw fastq -read data of bisulfite experiments; it produces reports on aggregate -methylation and coverage and can be used to produce information on -differential methylation and segmentation.") - (license gpl3+))) + `(("autoconf" ,(specification->package "autoconf")) + ("automake" ,(specification->package "automake")))))) -pigx-bsseq +pigx-bsseq-development