From 086c6800cfeb3db88bcd33badf5a6683ba4ce9db Mon Sep 17 00:00:00 2001
From: Lars-Dominik Braun <lars@6xq.net>
Date: Tue, 20 Jul 2021 11:50:31 +0200
Subject: gnu: checkm: Rename and update to 1.1.3.
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Renamed from python2-checkm-genome to checkm to better reflect its
status as standalone-application and support for Python 3.

* gnu/packages/bioinformatics.scm (python2-checkm-genome): Redirect to…
(checkm): …here and update to 1.1.3.
[propagated-inputs]: Move to inputs.
[inputs]: Use Python 3 dependencies.
[home-page]: Point to real home-page.
---
 gnu/packages/bioinformatics.scm | 33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e418b2cefd..8aa21c4fd6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13061,28 +13061,32 @@ downstream analysis.")
        ("taxtastic" ,taxtastic)))
     (synopsis "Pplacer Python scripts")))
 
-(define-public python2-checkm-genome
+(define-public checkm
   (package
-    (name "python2-checkm-genome")
-    (version "1.0.13")
+    (name "checkm")
+    (version "1.1.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "checkm-genome" version))
        (sha256
         (base32
-         "0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz"))))
+         "0i2nnki639hgjag17wlva2x0ymn37b4krqsf6akxddykhfbkdnkz"))))
     (build-system python-build-system)
     (arguments
-     `(#:python ,python-2
-       #:tests? #f))                    ; some tests are interactive
-    (propagated-inputs
-     `(("python-dendropy" ,python2-dendropy)
-       ("python-matplotlib" ,python2-matplotlib)
-       ("python-numpy" ,python2-numpy)
-       ("python-pysam" ,python2-pysam)
-       ("python-scipy" ,python2-scipy)))
-    (home-page "https://pypi.org/project/Checkm/")
+     `(#:tests? #f ; Some tests fail for unknown reasons.
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'set-HOME
+           (lambda _
+             (setenv "HOME" "/tmp"))))))
+    (inputs
+     `(("python-dendropy" ,python-dendropy)
+       ("python-matplotlib" ,python-matplotlib)
+       ("python-numpy" ,python-numpy)
+       ("python-pysam" ,python-pysam)
+       ("python-scipy" ,python-scipy)))
+    (home-page "https://ecogenomics.github.io/CheckM/")
     (synopsis "Assess the quality of putative genome bins")
     (description
      "CheckM provides a set of tools for assessing the quality of genomes
@@ -13097,6 +13101,9 @@ on marker set compatibility, similarity in genomic characteristics, and
 proximity within a reference genome.")
     (license license:gpl3+)))
 
+(define-public python2-checkm-genome
+  (deprecated-package "python2-checkm-genome" checkm))
+
 (define-public umi-tools
   (package
     (name "umi-tools")
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