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authorBen Woodcroft <donttrustben@gmail.com>2017-07-03 23:00:14 +1000
committerBen Woodcroft <donttrustben@gmail.com>2017-07-08 12:05:59 +1000
commit4732e6ee84fea4e58b8a62cad054b10966f4f6e6 (patch)
tree6e808b2b7abb09b4d954d045fbe916952006786a /gnu/packages
parentf2fa86cc82b5941bde63b666337eea59aa609e55 (diff)
downloadpatches-4732e6ee84fea4e58b8a62cad054b10966f4f6e6.tar
patches-4732e6ee84fea4e58b8a62cad054b10966f4f6e6.tar.gz
gnu: blast+: Update to 2.6.0.
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. Add patch. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python. * gnu/packages/patches/blast+-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm25
-rw-r--r--gnu/packages/patches/blast+-fix-makefile.patch15
2 files changed, 31 insertions, 9 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1dc5ffac3c..55c2975a1e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -956,7 +956,7 @@ package provides command line tools using the Bio++ library.")
(define-public blast+
(package
(name "blast+")
- (version "2.4.0")
+ (version "2.6.0")
(source (origin
(method url-fetch)
(uri (string-append
@@ -964,13 +964,15 @@ package provides command line tools using the Bio++ library.")
version "/ncbi-blast-" version "+-src.tar.gz"))
(sha256
(base32
- "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
+ "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
+ (patches (search-patches "blast+-fix-makefile.patch"))
(modules '((guix build utils)))
(snippet
'(begin
- ;; Remove bundled bzip2 and zlib
+ ;; Remove bundled bzip2, zlib and pcre.
(delete-file-recursively "c++/src/util/compress/bzip2")
(delete-file-recursively "c++/src/util/compress/zlib")
+ (delete-file-recursively "c++/src/util/regexp")
(substitute* "c++/src/util/compress/Makefile.in"
(("bzip2 zlib api") "api"))
;; Remove useless msbuild directory
@@ -979,9 +981,8 @@ package provides command line tools using the Bio++ library.")
#t))))
(build-system gnu-build-system)
(arguments
- `(;; There are three(!) tests for this massive library, and all fail with
+ `(;; There are two(!) tests for this massive library, and both fail with
;; "unparsable timing stats".
- ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
#:tests? #f
@@ -1014,6 +1015,7 @@ package provides command line tools using the Bio++ library.")
;; Rewrite hardcoded paths to various tools
(substitute* (append '("src/build-system/configure.ac"
"src/build-system/configure"
+ "src/build-system/helpers/run_with_lock.c"
"scripts/common/impl/if_diff.sh"
"scripts/common/impl/run_with_lock.sh"
"src/build-system/Makefile.configurables.real"
@@ -1062,17 +1064,22 @@ package provides command line tools using the Bio++ library.")
(assoc-ref inputs "bzip2"))
(string-append "--with-z="
(assoc-ref inputs "zlib"))
+ (string-append "--with-pcre="
+ (assoc-ref inputs "pcre"))
;; Each library is built twice by default, once
;; with "-static" in its name, and again
;; without.
"--without-static"
"--with-dll"))))))))
- (outputs '("out" ; 19 MB
- "lib" ; 203 MB
- "include")) ; 32 MB
+ (outputs '("out" ; 21 MB
+ "lib" ; 226 MB
+ "include")) ; 33 MB
(inputs
`(("bzip2" ,bzip2)
- ("zlib" ,zlib)))
+ ("zlib" ,zlib)
+ ("pcre" ,pcre)
+ ("perl" ,perl)
+ ("python" ,python-wrapper)))
(native-inputs
`(("cpio" ,cpio)))
(home-page "http://blast.ncbi.nlm.nih.gov")
diff --git a/gnu/packages/patches/blast+-fix-makefile.patch b/gnu/packages/patches/blast+-fix-makefile.patch
new file mode 100644
index 0000000000..bfa46a7e51
--- /dev/null
+++ b/gnu/packages/patches/blast+-fix-makefile.patch
@@ -0,0 +1,15 @@
+Without this patch, the 'make install' attempts to 'install' a directory, which causes an error.
+
+diff --git a/c++/src/build-system/Makefile.in.top b/c++/src/build-system/Makefile.in.top
+index 1abe44f..d6000b3 100644
+--- a/c++/src/build-system/Makefile.in.top
++++ b/c++/src/build-system/Makefile.in.top
+@@ -51,7 +51,7 @@ install-toolkit:
+ done
+ cd $(includedir0) && find * -name CVS -prune -o -print |\
+ cpio -pd $(pincludedir)
+- $(INSTALL) -m 644 $(incdir)/* $(pincludedir)
++ cp -R $(incdir)/* $(pincludedir)
+ ## set up appropriate build and status directories somewhere under $(libdir)?
+
+ install-gbench: