From 18dea67dc3a42d782b34b551304748346f173184 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Mon, 3 Jul 2017 23:00:14 +1000 Subject: gnu: blast+: Update to 2.6.0. * gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python. --- gnu/packages/bioinformatics.scm | 25 ++++++++++++++++--------- 1 file changed, 16 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d63647b15c..9fe4dc2b82 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -956,7 +956,7 @@ (define-public bppsuite (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 @@ (define-public blast+ 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 @@ (define-public blast+ #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 @@ (define (which* cmd) ;; 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 @@ (define (which* cmd) (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") -- cgit v1.2.3