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authorBen Woodcroft <donttrustben@gmail.com>2017-02-09 21:13:39 +1000
committerBen Woodcroft <donttrustben@gmail.com>2017-02-09 21:21:29 +1000
commit206af46fe1cc0627e4846167aa5e7c095b21afe3 (patch)
treedf744fa0a06d890d3c3baed843f9f765fdb705f6 /gnu/packages/bioinformatics.scm
parentc8916c3336154f1933a59883d4e1da9f23249a09 (diff)
gnu: vsearch: Update to 2.4.0.
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0. [source]: Convert most operations in the snippet to patch form and adjust for 2.4.0. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm29
1 files changed, 5 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d7089959ea..a448b51c6c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5748,7 +5748,7 @@ track. The database is exposed as a @code{TxDb} object.")
(define-public vsearch
(package
(name "vsearch")
- (version "2.3.4")
+ (version "2.4.0")
(source
(origin
(method url-fetch)
@@ -5758,31 +5758,12 @@ track. The database is exposed as a @code{TxDb} object.")
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1xyraxmhyx62mxx8z7c8waygvcijwkh48ms1ar60w2cv2y2sn4al"))
- (modules '((guix build utils)))
+ "007q9a50hdw4vs2iajabvbw7qccml4r8cbqzyi5ipkkf42jk3vnr"))
+ (patches (search-patches "vsearch-unbundle-cityhash.patch"))
(snippet
'(begin
- ;; Remove bundled cityhash and '-mtune=native'.
- (substitute* "src/Makefile.am"
- (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \
--O3 -mtune=native -Wall -Wsign-compare")
- (string-append "AM_CXXFLAGS=-lcityhash"
- " -O3 -Wall -Wsign-compare"))
- (("^__top_builddir__bin_vsearch_SOURCES = city.h \\\\")
- "__top_builddir__bin_vsearch_SOURCES = \\")
- (("^city.h \\\\") "\\")
- (("^citycrc.h \\\\") "\\")
- (("^libcityhash_a.*") "")
- (("noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a \
-libcityhash.a")
- "noinst_LIBRARIES = libcpu_sse2.a libcpu_ssse3.a")
- (("__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
-libcpu_sse2.a libcityhash.a")
- "__top_builddir__bin_vsearch_LDADD = libcpu_ssse3.a \
-libcpu_sse2.a -lcityhash"))
- (substitute* "src/vsearch.h"
- (("^\\#include \"city.h\"") "#include <city.h>")
- (("^\\#include \"citycrc.h\"") "#include <citycrc.h>"))
+ ;; Remove bundled cityhash sources. The vsearch source is adjusted
+ ;; for this in the patch.
(delete-file "src/city.h")
(delete-file "src/citycrc.h")
(delete-file "src/city.cc")