* [PATCH] Add Couger.
@ 2015-06-03 11:56 Ricardo Wurmus
2015-06-06 17:44 ` Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Ricardo Wurmus @ 2015-06-03 11:56 UTC (permalink / raw
To: guix-devel
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From d4f171912387304e61f2536a2eb167c7321e7663 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 2 Jun 2015 15:47:22 +0200
Subject: [PATCH 1/2] gnu: Add randomjungle.
* gnu/packages/machine-learning.scm (randomjungle): New variable.
---
gnu/packages/machine-learning.scm | 50 ++++++++++++++++++++++++++++++++++++++-
1 file changed, 49 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 3b4af19..37e1c94 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -23,7 +23,12 @@
#:use-module (guix download)
#:use-module (guix build-system gnu)
#:use-module (gnu packages)
- #:use-module (gnu packages python))
+ #:use-module (gnu packages boost)
+ #:use-module (gnu packages compression)
+ #:use-module (gnu packages gcc)
+ #:use-module (gnu packages maths)
+ #:use-module (gnu packages python)
+ #:use-module (gnu packages xml))
(define-public libsvm
(package
@@ -95,3 +100,46 @@ classification.")
#t)))))
(inputs
`(("python" ,python)))))
+
+(define-public randomjungle
+ (package
+ (name "randomjungle")
+ (version "2.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
+ "randomjungle-" version ".tar_.gz"))
+ (sha256
+ (base32
+ "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:configure-flags
+ (list (string-append "--with-boost="
+ (assoc-ref %build-inputs "boost")))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before
+ 'configure 'set-CXXFLAGS
+ (lambda _
+ (setenv "CXXFLAGS" "-fpermissive ")
+ #t)))))
+ (inputs
+ `(("boost" ,boost)
+ ("gsl" ,gsl)
+ ("libxml2" ,libxml2)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("gfortran" ,gfortran-4.8)))
+ (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
+ (synopsis "Implementation of the Random Forests machine learning method")
+ (description
+ "Random Jungle is an implementation of Random Forests. It is supposed to
+analyse high dimensional data. In genetics, it can be used for analysing big
+Genome Wide Association (GWA) data. Random Forests is a powerful machine
+learning method. Most interesting features are variable selection, missing
+value imputation, classifier creation, generalization error estimation and
+sample proximities between pairs of cases.")
+ (license license:gpl3+)))
--
2.1.0
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From c9246d7cfc56a0e4a9039a4b5e2dd9a7216ebeef Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 3 Jun 2015 12:56:16 +0200
Subject: [PATCH 2/2] gnu: Add Couger.
* gnu/packages/bioinformatics.scm (couger): New variable.
---
gnu/packages/bioinformatics.scm | 71 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 71 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index afcfecf..fd1c1dd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -34,6 +34,7 @@
#:use-module (gnu packages file)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
+ #:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
@@ -438,6 +439,76 @@ multiple sequence alignments.")
"CLIPper is a tool to define peaks in CLIP-seq datasets.")
(license license:gpl2)))
+(define-public couger
+ (package
+ (name "couger")
+ (version "1.8.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://couger.oit.duke.edu/static/assets/COUGER"
+ version ".zip"))
+ (sha256
+ (base32
+ "1bs151a54wnjl1bwnvlf31p17vs73vgiidnka3al02rmp1vrli8g"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'build)
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (copy-recursively "src" (string-append out "/src"))
+ (mkdir (string-append out "/bin"))
+ ;; Add "src" directory to module lookup path.
+ (substitute* "couger"
+ (("from argparse")
+ (string-append "import sys\nsys.path.append(\""
+ out "\")\nfrom argparse")))
+ (copy-file "couger" (string-append out "/bin/couger")))
+ #t))
+ (add-after
+ 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Make sure 'couger' runs with the correct PYTHONPATH.
+ (let* ((out (assoc-ref outputs "out"))
+ (path (getenv "PYTHONPATH")))
+ (wrap-program (string-append out "/bin/couger")
+ `("PYTHONPATH" ":" prefix (,path))))
+ #t)))))
+ (inputs
+ `(("python" ,python-2)
+ ("python2-pillow" ,python2-pillow)
+ ("python2-numpy" ,python2-numpy)
+ ("python2-scipy" ,python2-scipy)
+ ("python2-matplotlib" ,python2-matplotlib)))
+ (propagated-inputs
+ `(("r" ,r)
+ ("libsvm" ,libsvm)
+ ("randomjungle" ,randomjungle)))
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://couger.oit.duke.edu")
+ (synopsis "Identify co-factors in sets of genomic regions")
+ (description
+ "COUGER can be applied to any two sets of genomic regions bound by
+paralogous TFs (e.g., regions derived from ChIP-seq experiments) to identify
+putative co-factors that provide specificity to each TF. The framework
+determines the genomic targets uniquely-bound by each TF, and identifies a
+small set of co-factors that best explain the in vivo binding differences
+between the two TFs.
+
+COUGER uses classification algorithms (support vector machines and random
+forests) with features that reflect the DNA binding specificities of putative
+co-factors. The features are generated either from high-throughput TF-DNA
+binding data (from protein binding microarray experiments), or from large
+collections of DNA motifs.")
+ (license license:gpl3+)))
+
(define-public clustal-omega
(package
(name "clustal-omega")
--
2.1.0
^ permalink raw reply related [flat|nested] 2+ messages in thread
* Re: [PATCH] Add Couger.
2015-06-03 11:56 [PATCH] Add Couger Ricardo Wurmus
@ 2015-06-06 17:44 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2015-06-06 17:44 UTC (permalink / raw
To: Ricardo Wurmus; +Cc: guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
> From d4f171912387304e61f2536a2eb167c7321e7663 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 2 Jun 2015 15:47:22 +0200
> Subject: [PATCH 1/2] gnu: Add randomjungle.
>
> * gnu/packages/machine-learning.scm (randomjungle): New variable.
LGTM.
> From c9246d7cfc56a0e4a9039a4b5e2dd9a7216ebeef Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 3 Jun 2015 12:56:16 +0200
> Subject: [PATCH 2/2] gnu: Add Couger.
>
> * gnu/packages/bioinformatics.scm (couger): New variable.
LGTM.
Thanks!
Ludo'.
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2015-06-06 17:44 ` Ludovic Courtès
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