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| author | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-03 23:00:14 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2017-07-08 12:05:59 +1000 |
| commit | 4732e6ee84fea4e58b8a62cad054b10966f4f6e6 (patch) | |
| tree | 6e808b2b7abb09b4d954d045fbe916952006786a /gnu/packages/bioinformatics.scm | |
| parent | f2fa86cc82b5941bde63b666337eea59aa609e55 (diff) | |
| download | gnu-guix-4732e6ee84fea4e58b8a62cad054b10966f4f6e6.tar gnu-guix-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/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 |
1 files changed, 16 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") |