From 39fb853abe060973c0ca6f8b60a105b1a83e583b Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Tue, 9 Jan 2018 22:18:06 +1000
Subject: gnu: seqmagick: Update to 0.7.0.

* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0.  Use
python-3.
[arguments]: Remove replacement phase for check.
[inputs]: Add biopython.  Remove python2-biopython-1.66.
(python2-biopython-1.66): Remove variable.
---
 gnu/packages/bioinformatics.scm | 35 ++++-------------------------------
 1 file changed, 4 insertions(+), 31 deletions(-)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ce66ce0d37..34b843cfbb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -790,20 +790,6 @@ into separate processes; and more.")
 (define-public python2-biopython
   (package-with-python2 python-biopython))
 
-;; An outdated version of biopython is required for seqmagick, see
-;; https://github.com/fhcrc/seqmagick/issues/59
-;; When that issue has been resolved this package should be removed.
-(define python2-biopython-1.66
-  (package
-    (inherit python2-biopython)
-    (version "1.66")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "biopython" version))
-              (sha256
-               (base32
-                "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))))
-
 (define-public bpp-core
   ;; The last release was in 2014 and the recommended way to install from source
   ;; is to clone the git repository, so we do this.
@@ -5391,7 +5377,7 @@ bioinformatics file formats, sequence alignment, and more.")
 (define-public seqmagick
   (package
     (name "seqmagick")
-    (version "0.6.1")
+    (version "0.7.0")
     (source
      (origin
        (method url-fetch)
@@ -5400,25 +5386,12 @@ bioinformatics file formats, sequence alignment, and more.")
              version ".tar.gz"))
        (sha256
         (base32
-         "0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
+         "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
     (build-system python-build-system)
-    (arguments
-     ;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
-     `(#:python ,python-2
-       #:phases
-       (modify-phases %standard-phases
-         ;; Current test in setup.py does not work as of 0.6.1,
-         ;; so use nose to run tests instead for now. See
-         ;; https://github.com/fhcrc/seqmagick/issues/55
-         (replace 'check (lambda _ (zero? (system* "nosetests")))))))
     (inputs
-     ;; biopython-1.66 is required due to
-     ;; https://github.com/fhcrc/seqmagick/issues/59
-     ;; When that issue is resolved the 'python2-biopython-1.66' package
-     ;; should be removed.
-     `(("python-biopython" ,python2-biopython-1.66)))
+     `(("python-biopython" ,python-biopython)))
     (native-inputs
-     `(("python-nose" ,python2-nose)))
+     `(("python-nose" ,python-nose)))
     (home-page "https://github.com/fhcrc/seqmagick")
     (synopsis "Tools for converting and modifying sequence files")
     (description
-- 
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