From 94d0efffb39878440bcac564a0ce18c7af3de64f Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 5 May 2023 22:32:05 +0200
Subject: Revert "gnu: Add python-gimmemotifs."

This reverts commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47.

python-gimmemotifs is not usable without proprietary third-party tools.
---
 gnu/packages/bioinformatics.scm | 76 -----------------------------------------
 1 file changed, 76 deletions(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 241b99f23d..e48b340a3a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -86,7 +86,6 @@ (define-module (gnu packages bioinformatics)
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
-  #:use-module (gnu packages digest)
   #:use-module (gnu packages dlang)
   #:use-module (gnu packages file)
   #:use-module (gnu packages flex)
@@ -5292,81 +5291,6 @@ (define-public python-genomepy
 All with sensible, yet controllable defaults.")
     (license license:expat)))
 
-(define-public python-gimmemotifs
-  (package
-    (name "python-gimmemotifs")
-    (version "0.18.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/vanheeringen-lab/gimmemotifs/")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "0jxr8884k7lic88vhr35l59q5qlpm64p4sv3xfq3l4y41ansh2z0"))
-              (modules '((guix build utils)))
-              ;; Delete included third-party binaries
-              (snippet
-               '(delete-file-recursively "src"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; A lot of the tests depend on a wide range of external tools.
-      '(list "--ignore=test/test_02_config.py"
-             "--ignore=test/test_06_moap.py"
-             "--ignore=test/test_06_stats.py"
-             "--ignore=test/test_08_denovo.py"
-             "--ignore=test/test_08_maelstrom.py"
-             "--ignore=test/test_08_prediction.py"
-             "--ignore=test/test_09_cli.py"
-             "-k"
-             (string-append "not test_tool"
-                            ;; not needed
-                            " and not test_black_formatting"
-                            " and not test_flake8_formatting"
-                            " and not test_isort_formatting"))
-      #:phases
-      '(modify-phases %standard-phases
-         (add-after 'unpack 'do-not-copy-binaries
-           (lambda _
-             (substitute* "setup.py"
-               (("^cmdclass\\[\"build_py.*") ""))))
-         (add-after 'unpack 'set-HOME
-           (lambda _ (setenv "HOME" "/tmp")))
-         ;; This fails because there is no configuration file to load.
-         (delete 'sanity-check))))
-    (propagated-inputs (list python-biofluff
-                             python-configparser
-                             python-diskcache
-                             python-feather-format
-                             python-genomepy
-                             python-iteround
-                             python-jinja2
-                             python-logomaker
-                             python-loguru
-                             python-matplotlib
-                             python-numpy
-                             python-pandas
-                             python-pybedtools
-                             python-pysam
-                             python-qnorm
-                             python-scikit-learn
-                             python-scipy
-                             python-seaborn
-                             python-setuptools
-                             python-statsmodels
-                             python-tqdm
-                             python-xdg
-                             python-xxhash))
-    (native-inputs (list python-pytest))
-    (home-page "https://github.com/vanheeringen-lab/gimmemotifs/")
-    (synopsis "GimmeMotifs is a motif prediction pipeline.")
-    (description "GimmeMotifs is a suite of motif tools, including a motif
-prediction pipeline for ChIP-seq experiments.")
-    (license license:expat)))
-
 (define-public java-htsjdk
   (package
     (name "java-htsjdk")
-- 
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