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| author | Ricardo Wurmus <rekado@elephly.net> | 2017-01-16 11:56:00 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2017-01-17 21:46:48 +0100 |
| commit | 769fc6bb18d311bafa47e9666d35db2cb594e8ab (patch) | |
| tree | 0294224bb380cae43179918bcd5805c92653da5e | |
| parent | e84efc50d7156706fbf6fc86065371b67f929289 (diff) | |
| download | patches-769fc6bb18d311bafa47e9666d35db2cb594e8ab.tar patches-769fc6bb18d311bafa47e9666d35db2cb594e8ab.tar.gz | |
gnu: Add ribodiff.
* gnu/packages/bioinformatics.scm (ribodiff): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b3aedec63f..cd64d34390 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") |