From d53679c5317f4a2d11876696b3880edf1f76ff1b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 2 Dec 2021 00:30:48 +0100
Subject: gnu: Remove couger.

This package has been moved to the Guix Past channel.

* gnu/packages/bioinformatics.scm (couger): Remove variable.
---
 gnu/packages/bioinformatics.scm | 71 -----------------------------------------
 1 file changed, 71 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dffd59d863..aa156b6287 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2721,77 +2721,6 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.")
     (home-page "https://sourceforge.net/projects/codingquarry/")
     (license license:gpl3+)))
 
-(define-public couger
-  (package
-    (name "couger")
-    (version "1.8.2")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "http://couger.oit.duke.edu/static/assets/COUGER"
-                    version ".zip"))
-              (sha256
-               (base32
-                "04p2b14nmhzxw5h72mpzdhalv21bx4w9b87z0wpw0xzxpysyncmq"))))
-    (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"))
-                   (bin (string-append out "/bin")))
-              (copy-recursively "src" (string-append out "/src"))
-              (mkdir bin)
-              ;; Add "src" directory to module lookup path.
-              (substitute* "couger"
-                (("from argparse")
-                 (string-append "import sys\nsys.path.append(\""
-                                out "\")\nfrom argparse")))
-              (install-file "couger" bin))
-            #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-minimal" ,r-minimal)
-       ("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")
-- 
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