From 176513f5f3d09f9604a601fab7ba193e95a29c35 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Mon, 7 Jun 2021 11:35:27 +0200
Subject: gnu: jellyfish: Update to 2.3.0.

* gnu/packages/bioinformatics.scm (jellyfish): Update to 2.3.0.
[arguments]: Disable SSE to avoid tuning to the build node's CPU.
[native-inputs]: Replace python-2 with python-wrapper.
[license]: Update.
---
 gnu/packages/bioinformatics.scm | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 788e7ae836..365a30c166 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4715,7 +4715,7 @@ experiments and provide highly stable thresholds based on reproducibility.")
 (define-public jellyfish
   (package
     (name "jellyfish")
-    (version "2.2.10")
+    (version "2.3.0")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://github.com/gmarcais/Jellyfish/"
@@ -4723,14 +4723,15 @@ experiments and provide highly stable thresholds based on reproducibility.")
                                   "/jellyfish-" version ".tar.gz"))
               (sha256
                (base32
-                "1k4pc3fvv6w1km2yph4m5sd78fbxp21d6xyzgmy0gjihzc6mb249"))))
+                "0npa62wzasdibas5zp3n8j3armsci4kyvh0jw7jr0am4gg7vg5g1"))))
     (build-system gnu-build-system)
     (outputs '("out"      ;for library
                "ruby"     ;for Ruby bindings
                "python")) ;for Python bindings
     (arguments
      `(#:configure-flags
-       (list (string-append "--enable-ruby-binding="
+       (list "--without-sse" ; configure script probes for CPU features when SSE is enabled.
+             (string-append "--enable-ruby-binding="
                             (assoc-ref %outputs "ruby"))
              (string-append "--enable-python-binding="
                             (assoc-ref %outputs "python")))
@@ -4740,13 +4741,12 @@ experiments and provide highly stable thresholds based on reproducibility.")
            (lambda _
              ;; generator_manager.hpp either uses /bin/sh or $SHELL
              ;; to run tests.
-             (setenv "SHELL" (which "bash"))
-             #t)))))
+             (setenv "SHELL" (which "bash")))))))
     (native-inputs
      `(("bc" ,bc)
        ("time" ,time)
        ("ruby" ,ruby)
-       ("python" ,python-2)
+       ("python" ,python-wrapper)
        ("pkg-config" ,pkg-config)))
     (inputs
      `(("htslib" ,htslib)))
@@ -4762,9 +4762,8 @@ command, or queried for specific k-mers with @code{jellyfish query}.")
     (home-page "http://www.genome.umd.edu/jellyfish.html")
     ;; JELLYFISH seems to be 64-bit only.
     (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
-    ;; The combined work is published under the GPLv3 or later.  Individual
-    ;; files such as lib/jsoncpp.cpp are released under the Expat license.
-    (license (list license:gpl3+ license:expat))))
+    ;; One of these licenses may be picked
+    (license (list license:gpl3+ license:bsd-3))))
 
 (define-public khmer
   (package
-- 
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