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author | pimi <madalinionel.patrascu@mdc-berlin.de> | 2018-10-08 11:17:41 +0200 |
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committer | Ludovic Courtès <ludo@gnu.org> | 2018-10-08 18:32:42 +0200 |
commit | b6bd8b108a4ad53e89d6b83edc57df18935f131c (patch) | |
tree | aa0b3936efd2c617c44ace2552b26331dcfc6720 /gnu/packages | |
parent | f8e0d27c5c2f338012f00cd3c4620ca76751495c (diff) | |
download | guix-patches-b6bd8b108a4ad53e89d6b83edc57df18935f131c.tar guix-patches-b6bd8b108a4ad53e89d6b83edc57df18935f131c.tar.gz |
gnu: Add filtlong.
* gnu/packages/bioinformatics.scm (filtlong): New variable.
Co-authored-by: Ludovic Courtès <ludo@gnu.org>
Diffstat (limited to 'gnu/packages')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 60 |
1 files changed, 60 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ab9dc185a3..ed713cd144 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14057,3 +14057,63 @@ absolute GSEA.") (description "Ngless is a domain-specific language for @dfn{next-generation sequencing} (NGS) data processing.") (license license:expat))) + +(define-public filtlong + ;; The recommended way to install is to clone the git repository + ;; https://github.com/rrwick/Filtlong#installation + ;; and the lastest release is more than nine months old + (let ((commit "d1bb46dfe8bc7efe6257b5ce222c04bfe8aedaab") + (revision "1")) + (package + (name "filtlong") + (version (git-version "0.2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Filtlong.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xr92r820x8qlkcr3b57iw223yq8vjgyi42jr79w2xgw47qzr575")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; no check target + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (scripts (string-append out "/share/filtlong/scripts"))) + (install-file "bin/filtlong" bin) + (install-file "scripts/histogram.py" scripts) + (install-file "scripts/read_info_histograms.sh" scripts)) + #t)) + (add-after 'install 'wrap-program + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (path (getenv "PYTHONPATH"))) + (wrap-program (string-append out + "/share/filtlong/scripts/histogram.py") + `("PYTHONPATH" ":" prefix (,path)))) + #t)) + (add-before 'check 'patch-tests + (lambda _ + (substitute* "scripts/read_info_histograms.sh" + (("awk") (which "gawk"))) + #t))))) + (inputs + `(("gawk" ,gawk) ;for read_info_histograms.sh + ("python" ,python-2) ;required for histogram.py + ("zlib" ,zlib))) + (home-page "https://github.com/rrwick/Filtlong/") + (synopsis "Tool for quality filtering of Nanopore and PacBio data") + (description + "The Filtlong package is a tool for filtering long reads by quality. +It can take a set of long reads and produce a smaller, better subset. It uses +both read length (longer is better) and read identity (higher is better) when +choosing which reads pass the filter.") + (license (list license:gpl3 ;filtlong + license:asl2.0))))) ;histogram.py |