pimi wrote 6 years ago
(address . guix-patches@gnu.org)(address . ricardo.wurmus@mdc-berlin.de)(name . pimi)(address . madalinionel.patrascu@mdc-berlin.de)
20181008091741.31531-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (filtlong): New variable.
---
gnu/packages/bioinformatics.scm | 63 +++++++++++++++++++++++++++++++++
1 file changed, 63 insertions(+)
Toggle diff (73 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ab9dc185a..43cdf811e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -14057,3 +14057,66 @@ 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"))))
+ ;;(properties `((upstream-name . "Filtlong")))
+ (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 "/scripts")))
+ (mkdir-p bin)
+ (mkdir-p 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-apend scripts "scripts/read_info_histograms.sh")
+ (wrap-program (string-append out "/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 @code{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
--
2.17.1