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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.
This commit is contained in:
Ben Woodcroft 2017-07-03 23:00:14 +10:00
parent c24ea83cd7
commit 18dea67dc3
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GPG Key ID: 2A6AD9F4AAC20DF6
1 changed files with 16 additions and 9 deletions
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gnu/packages/bioinformatics.scm
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@ -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")