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authorRicardo Wurmus <rekado@elephly.net>2017-04-13 14:16:32 +0200
committerRicardo Wurmus <rekado@elephly.net>2017-06-09 03:31:50 +0200
commit44f6c88909061bb37facc180f3af948a55eb3caa (patch)
treef2d4c162b1e27aa430e442f683ef820ee5984f99
parentb8fffd3a53a6b588e3613272802db580994b9cb0 (diff)
downloadguix-44f6c88909061bb37facc180f3af948a55eb3caa.tar
guix-44f6c88909061bb37facc180f3af948a55eb3caa.tar.gz
gnu: Add trim-galore.
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm60
1 files changed, 60 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d61f91fcad..fbff587302 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9268,3 +9268,63 @@ signal processing that can accurately call binding events without the need to
do a pair total DNA input or IgG control sample. It has been tested for use
with narrow binding events such as transcription factor ChIP-seq.")
(license license:gpl3+)))
+
+(define-public trim-galore
+ (package
+ (name "trim-galore")
+ (version "0.4.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.bioinformatics.babraham.ac.uk/"
+ "projects/trim_galore/trim_galore_v"
+ version ".zip"))
+ (sha256
+ (base32
+ "0b9qdxi4521gsrjvbhgky8g7kry9b5nx3byzaxkgxz7p4k8bn1mn"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no tests
+ #:phases
+ (modify-phases %standard-phases
+ ;; The archive contains plain files.
+ (replace 'unpack
+ (lambda* (#:key source #:allow-other-keys)
+ (zero? (system* "unzip" source))))
+ (delete 'configure)
+ (delete 'build)
+ (add-after 'unpack 'hardcode-tool-references
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "trim_galore"
+ (("\\$path_to_cutadapt = 'cutadapt'")
+ (string-append "$path_to_cutadapt = '"
+ (assoc-ref inputs "cutadapt")
+ "/bin/cutadapt'"))
+ (("\\| gzip")
+ (string-append "| "
+ (assoc-ref inputs "gzip")
+ "/bin/gzip"))
+ (("\"gunzip")
+ (string-append "\""
+ (assoc-ref inputs "gzip")
+ "/bin/gunzip")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out")
+ "/bin")))
+ (mkdir-p bin)
+ (install-file "trim_galore" bin)
+ #t))))))
+ (inputs
+ `(("gzip" ,gzip)
+ ("perl" ,perl)
+ ("cutadapt" ,cutadapt)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/")
+ (synopsis "Wrapper around Cutadapt and FastQC")
+ (description "Trim Galore! is a wrapper script to automate quality and
+adapter trimming as well as quality control, with some added functionality to
+remove biased methylation positions for RRBS sequence files.")
+ (license license:gpl3+)))