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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-02-19 22:47:26 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-02-19 23:14:59 +0100 |
| commit | 15c0cc4aa2bc27145c29a5ebb9a0387866d01826 (patch) | |
| tree | 0bcc8a81c7623e41af36519320732354a4c71093 | |
| parent | 113dabe831f5df1f5a745ee3c68c5ccd158e7141 (diff) | |
| download | guix-15c0cc4aa2bc27145c29a5ebb9a0387866d01826.tar guix-15c0cc4aa2bc27145c29a5ebb9a0387866d01826.tar.gz | |
gnu: Add prinseq.
* gnu/packages/bioinformatics.scm (prinseq): 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 a84c1c812c..7d5521e91d 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") |