From: Ben Woodcroft <donttrustben@gmail.com>
To: guix-devel@gnu.org
Subject: [PATCH] gnu: Add proteinortho.
Date: Sat, 26 Nov 2016 15:14:16 +1000 [thread overview]
Message-ID: <20161126051416.12616-1-donttrustben@gmail.com> (raw)
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
---
gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 52 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 773b590..31e9533 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3693,6 +3693,58 @@ for sequences to be aligned and then, simultaneously with the alignment,
predicts the locations of structural units in the sequences.")
(license license:gpl2+)))
+(define-public proteinortho
+ (package
+ (name "proteinortho")
+ (version "5.15")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "http://www.bioinf.uni-leipzig.de/Software/proteinortho/proteinortho_v"
+ version "_src.tar.gz"))
+ (sha256
+ (base32
+ "05wacnnbx56avpcwhzlcf6b7s77swcpv3qnwz5sh1z54i51gg2ki"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:test-target "test"
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ ;; There is no configure script, so we modify the Makefile directly.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("INSTALLDIR=.*")
+ (string-append
+ "INSTALLDIR=" (assoc-ref outputs "out") "/bin")))
+ #t))
+ (add-before 'install 'make-install-directory
+ ;; The install directory is not created during 'make install'.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir-p (string-append (assoc-ref outputs "out") "/bin"))
+ #t))
+ (add-after 'install 'wrap-programs
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((path (getenv "PATH"))
+ (out (assoc-ref outputs "out"))
+ (binary (string-append out "/bin/proteinortho5.pl")))
+ (wrap-program binary `("PATH" ":" prefix (,path))))
+ #t)))))
+ (inputs
+ `(("perl" ,perl)
+ ("python" ,python-2)
+ ("blast+" ,blast+)))
+ (home-page "http://www.bioinf.uni-leipzig.de/Software/proteinortho")
+ (synopsis "Detect orthologous genes across species")
+ (description
+ "Proteinortho is a tool to detect orthologous genes across different
+species. For doing so, it compares similarities of given gene sequences and
+clusters them to find significant groups. The algorithm was designed to handle
+large-scale data and can be applied to hundreds of species at once.")
+ (license license:gpl2+)))
+
(define-public pyicoteo
(package
(name "pyicoteo")
--
2.10.2
next reply other threads:[~2016-11-26 5:14 UTC|newest]
Thread overview: 3+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-11-26 5:14 Ben Woodcroft [this message]
2016-11-26 6:11 ` [PATCH] gnu: Add proteinortho Leo Famulari
2016-11-26 10:23 ` Ben Woodcroft
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20161126051416.12616-1-donttrustben@gmail.com \
--to=donttrustben@gmail.com \
--cc=guix-devel@gnu.org \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.