forked from aslihankarabacak/FootprintPipeline
/
guix.scm
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guix.scm
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;;; Footprint pipeline -- Find transcription factor footprints.
;;; Copyright © 2017 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of the footprint pipeline.
;;;
;;; The footprint pipeline is free software; see COPYING file for details.
;;;
;;; Run the following command to enter a development environment:
;;;
;;; $ guix environment -l guix.scm --ad-hoc autoconf automake
;;;
;;; To install the package from a release tarball do this:
;;;
;;; $ guix package --with-source=footprint-pipeline-1.0.1.tar.gz -f guix.scm
;;;
;;; This environment file was developed for Guix version
;;; v0.13.0-4697-gef2c6b409
(use-modules (guix packages)
(guix licenses)
(guix download)
(guix build-system ant)
(guix build-system gnu)
(gnu packages)
(gnu packages statistics)
(gnu packages bioinformatics)
(gnu packages cran)
(gnu packages perl))
(define-public samtools-1.1
(package
(inherit samtools-0.1)
(version "1.1")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/samtools/samtools/"
version "/samtools-" version ".tar.bz2"))
(sha256
(base32
"1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))))
(define %fp-version
(symbol->string (with-input-from-file "VERSION" read)))
(define-public footprint-pipeline
(package
(name "footprint-pipeline")
(version %fp-version)
(source (string-append (getcwd) "/footprint-pipeline-" version ".tar.gz"))
(build-system gnu-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'install 'wrap-executable
(lambda* (#:key inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(wrap-program (string-append out "/bin/find_footprints.sh")
`("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE")))))
#t)))))
(inputs
`(("r-minimal" ,r-minimal)
("r-mixtools" ,r-mixtools)
("r-gtools" ,r-gtools)
("r-genomicranges" ,r-genomicranges)
("perl" ,perl)
("samtools" ,samtools-1.1)
("bedtools" ,bedtools-2.18)))
(home-page "https://ohlerlab.mdc-berlin.de/software/Reproducible_footprinting_139/")
(synopsis "Find transcription factor footprints in ATAC-seq or DNase-seq data")
(description "This is a pipeline to find transcription factor
footprints in ATAC-seq or DNase-seq data.")
(license gpl2+)))
footprint-pipeline