From: Ricardo Wurmus <rekado@elephly.net>
To: guix-devel@gnu.org
Subject: [PATCH 03/16] gnu: Add ribodiff.
Date: Tue, 17 Jan 2017 15:11:28 +0100 [thread overview]
Message-ID: <20170117141141.11694-4-rekado@elephly.net> (raw)
In-Reply-To: <20170117141141.11694-1-rekado@elephly.net>
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
---
gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b3aedec63..cd64d3439 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -468,6 +468,47 @@ frames} (ORFs) using ribosome profiling (ribo-seq) data. This package
provides the Ribotaper pipeline.")
(license license:gpl3+)))
+(define-public ribodiff
+ (package
+ (name "ribodiff")
+ (version "0.2.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/ratschlab/RiboDiff/"
+ "archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0wpbwmfv05wdjxv7ikm664f7s7p7cqr8jnw99zrda0q67rl50aaj"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ ;; Generate an installable executable script wrapper.
+ (add-after 'unpack 'patch-setup.py
+ (lambda _
+ (substitute* "setup.py"
+ (("^(.*)packages=.*" line prefix)
+ (string-append line "\n"
+ prefix "scripts=['scripts/TE.py'],\n")))
+ #t)))))
+ (inputs
+ `(("python-numpy" ,python2-numpy)
+ ("python-matplotlib" ,python2-matplotlib)
+ ("python-scipy" ,python2-scipy)
+ ("python-statsmodels" ,python2-statsmodels)))
+ (home-page "http://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
+ (synopsis "Detect translation efficiency changes from ribosome footprints")
+ (description "RiboDiff is a statistical tool that detects the protein
+translational efficiency change from Ribo-Seq (ribosome footprinting) and
+RNA-Seq data. It uses a generalized linear model to detect genes showing
+difference in translational profile taking mRNA abundance into account. It
+facilitates us to decipher the translational regulation that behave
+independently with transcriptional regulation.")
+ (license license:gpl3+)))
+
(define-public bioawk
(package
(name "bioawk")
--
2.11.0
next prev parent reply other threads:[~2017-01-17 14:12 UTC|newest]
Thread overview: 28+ messages / expand[flat|nested] mbox.gz Atom feed top
2017-01-17 14:11 [PATCH 00/16] Bioinfo stuff Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 01/16] gnu: Add python-argparse Ricardo Wurmus
2017-01-17 14:49 ` Hartmut Goebel
2017-01-17 15:26 ` Ricardo Wurmus
2017-01-17 18:48 ` Alex Kost
2017-01-17 18:47 ` Alex Kost
2017-01-17 14:11 ` [PATCH 02/16] gnu: Add hisat2 Ricardo Wurmus
2017-01-17 20:36 ` Leo Famulari
2017-01-17 20:49 ` Ricardo Wurmus
2017-01-17 14:11 ` Ricardo Wurmus [this message]
2017-01-17 14:11 ` [PATCH 04/16] gnu: Add r-compquadform Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 05/16] gnu: Add r-seqminer Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 06/16] gnu: Add r-raremetals2 Ricardo Wurmus
2017-01-20 13:16 ` Ludovic Courtès
2017-01-20 14:18 ` Ricardo Wurmus
2017-01-20 21:26 ` Ludovic Courtès
2017-01-17 14:11 ` [PATCH 07/16] gnu: Add r-maldiquant Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 08/16] gnu: Add r-protgenerics Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 09/16] gnu: Add r-mzr Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 10/16] gnu: Add r-affyio Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 11/16] gnu: Add r-affy Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 12/16] gnu: Add r-vsn Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 13/16] gnu: Add r-mzid Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 14/16] gnu: Add r-pcamethods Ricardo Wurmus
2017-01-17 14:11 ` [PATCH 15/16] gnu: Add r-msnbase Ricardo Wurmus
2017-01-20 13:17 ` Ludovic Courtès
2017-01-20 13:18 ` Ludovic Courtès
2017-01-17 14:11 ` [PATCH 16/16] gnu: Add r-msnid Ricardo Wurmus
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
List information: https://guix.gnu.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=20170117141141.11694-4-rekado@elephly.net \
--to=rekado@elephly.net \
--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 public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).