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| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-02-09 21:13:39 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-02-09 21:21:29 +1000 |
| commit | 206af46fe1cc0627e4846167aa5e7c095b21afe3 (patch) | |
| tree | df744fa0a06d890d3c3baed843f9f765fdb705f6 /gnu/packages/bioinformatics.scm | |
| parent | c8916c3336154f1933a59883d4e1da9f23249a09 (diff) | |
| download | patches-206af46fe1cc0627e4846167aa5e7c095b21afe3.tar patches-206af46fe1cc0627e4846167aa5e7c095b21afe3.tar.gz | |
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.scm | 29 |
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") |