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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.
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1 changed files with 16 additions and 9 deletions
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@ -956,7 +956,7 @@ (define-public bppsuite
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(define-public blast+
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(package
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(name "blast+")
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(version "2.4.0")
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(version "2.6.0")
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(source (origin
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(method url-fetch)
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(uri (string-append
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@ -964,13 +964,15 @@ (define-public blast+
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version "/ncbi-blast-" version "+-src.tar.gz"))
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(sha256
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(base32
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"14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb"))
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"15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405"))
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(patches (search-patches "blast+-fix-makefile.patch"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Remove bundled bzip2 and zlib
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;; Remove bundled bzip2, zlib and pcre.
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(delete-file-recursively "c++/src/util/compress/bzip2")
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(delete-file-recursively "c++/src/util/compress/zlib")
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(delete-file-recursively "c++/src/util/regexp")
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(substitute* "c++/src/util/compress/Makefile.in"
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(("bzip2 zlib api") "api"))
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;; Remove useless msbuild directory
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@ -979,9 +981,8 @@ (define-public blast+
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#t))))
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(build-system gnu-build-system)
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(arguments
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`(;; There are three(!) tests for this massive library, and all fail with
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`(;; There are two(!) tests for this massive library, and both fail with
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;; "unparsable timing stats".
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;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats)
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;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats)
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;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats)
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#:tests? #f
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@ -1014,6 +1015,7 @@ (define (which* cmd)
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;; Rewrite hardcoded paths to various tools
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(substitute* (append '("src/build-system/configure.ac"
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"src/build-system/configure"
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"src/build-system/helpers/run_with_lock.c"
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"scripts/common/impl/if_diff.sh"
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"scripts/common/impl/run_with_lock.sh"
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"src/build-system/Makefile.configurables.real"
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@ -1062,17 +1064,22 @@ (define (which* cmd)
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(assoc-ref inputs "bzip2"))
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(string-append "--with-z="
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(assoc-ref inputs "zlib"))
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(string-append "--with-pcre="
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(assoc-ref inputs "pcre"))
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;; Each library is built twice by default, once
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;; with "-static" in its name, and again
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;; without.
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"--without-static"
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"--with-dll"))))))))
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(outputs '("out" ; 19 MB
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"lib" ; 203 MB
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"include")) ; 32 MB
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(outputs '("out" ; 21 MB
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"lib" ; 226 MB
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"include")) ; 33 MB
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(inputs
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`(("bzip2" ,bzip2)
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("zlib" ,zlib)))
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("zlib" ,zlib)
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("pcre" ,pcre)
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("perl" ,perl)
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("python" ,python-wrapper)))
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(native-inputs
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`(("cpio" ,cpio)))
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(home-page "http://blast.ncbi.nlm.nih.gov")
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