diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 25 | ||||
| -rw-r--r-- | gnu/packages/patches/blast+-fix-makefile.patch | 15 |
3 files changed, 32 insertions, 9 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 8e4af46428..1bcd790f26 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -522,6 +522,7 @@ dist_patch_DATA = \ %D%/packages/patches/binutils-ld-new-dtags.patch \ %D%/packages/patches/binutils-loongson-workaround.patch \ %D%/packages/patches/binutils-mips-bash-bug.patch \ + %D%/packages/patches/blast+-fix-makefile.patch \ %D%/packages/patches/byobu-writable-status.patch \ %D%/packages/patches/cairo-CVE-2016-9082.patch \ %D%/packages/patches/calibre-drop-unrar.patch \ 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: |