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03/03: gnu: Add prinseq.
From: |
guix-commits |
Subject: |
03/03: gnu: Add prinseq. |
Date: |
Fri, 19 Feb 2021 17:16:58 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 15c0cc4aa2bc27145c29a5ebb9a0387866d01826
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Feb 19 22:47:26 2021 +0100
gnu: Add prinseq.
* gnu/packages/bioinformatics.scm (prinseq): 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 a84c1c8..7d5521e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7850,6 +7850,54 @@ for small genomes (such as those of RNA viruses like
HIV-1 and HCV) that
experience substantial biological insertions and deletions.")
(license license:gpl2+)))
+(define-public prinseq
+ (package
+ (name "prinseq")
+ (version "0.20.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/prinseq/standalone/"
+ "prinseq-lite-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0vxmzvmm67whxrqdaaamwgjk7cf0fzfs5s673jgg00kz7g70splv"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #false ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (for-each (lambda (file)
+ (chmod file #o555)
+ (install-file file bin)
+ (wrap-script (string-append bin "/" (basename file))
+ `("PERL5LIB" ":" prefix
+ (,(getenv "PERL5LIB")))))
+ (find-files "." "prinseq.*.pl"))))))))
+ (inputs
+ `(("guile" ,guile-3.0) ; for wrapper scripts
+ ("perl" ,perl)
+ ("perl-cairo" ,perl-cairo)
+ ("perl-data-dumper" ,perl-data-dumper)
+ ("perl-digest-md5" ,perl-digest-md5)
+ ("perl-getopt-long" ,perl-getopt-long)
+ ("perl-json" ,perl-json)
+ ("perl-statistics-pca" ,perl-statistics-pca)))
+ (home-page "http://prinseq.sourceforge.net/")
+ (synopsis "Preprocess sequence data in FASTA or FASTQ formats")
+ (description
+ "PRINSEQ is a bioinformatics tool to help you preprocess your genomic or
+metagenomic sequence data in FASTA or FASTQ formats. The tool is written in
+Perl and can be helpful if you want to filter, reformat, or trim your sequence
+data. It also generates basic statistics for your sequences.")
+ (license license:gpl3+)))
+
(define-public ruby-bio-kseq
(package
(name "ruby-bio-kseq")