gnu: blast+: Update to 2.14.0.
* gnu/packages/bioinformatics.scm (blast+): Update to 2.14.0. [arguments]: Remove trailing #T from build phases; let WHICH* return #FALSE on failure; use G-expression. [inputs]: Drop package labels.
This commit is contained in:
Ricardo Wurmus
parent
28bfc5cd08
commit
68ccd1a0d8
@ -2474,7 +2474,7 @@ package provides command line tools using the Bio++ library.")
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(define-public blast+
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(package
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(name "blast+")
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(version "2.11.0")
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(version "2.14.0")
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(source (origin
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(method url-fetch)
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(uri (string-append
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@ -2482,7 +2482,7 @@ package provides command line tools using the Bio++ library.")
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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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"0m0r9vkw631ky1za1wilsfk9k9spwqh22nkrb9a57rbwmrc1i3nq"))
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"003mn7m4y306k7visv3in3ikfgm8m41z0jq9lyvz10iv1hdpyixz"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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@ -2518,103 +2518,101 @@ package provides command line tools using the Bio++ library.")
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(("cksum") "cksum >/dev/null"))))))
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(build-system gnu-build-system)
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(arguments
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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] -- [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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#:out-of-source? #t
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#:parallel-build? #f ; not supported
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#:phases
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(modify-phases %standard-phases
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(add-before 'configure 'set-HOME
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;; $HOME needs to be set at some point during the configure phase
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(lambda _ (setenv "HOME" "/tmp") #t))
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(add-after 'unpack 'enter-dir
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(lambda _ (chdir "c++") #t))
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(add-after 'enter-dir 'fix-build-system
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(lambda _
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(define (which* cmd)
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(cond ((string=? cmd "date")
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;; make call to "date" deterministic
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"date -d @0")
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((which cmd)
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=> identity)
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(else
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(format (current-error-port)
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"WARNING: Unable to find absolute path for ~s~%"
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cmd)
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#f)))
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(list
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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] -- [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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#:out-of-source? #t
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#:parallel-build? #f ;not supported
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#:phases
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#~(modify-phases %standard-phases
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(add-before 'configure 'set-HOME
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;; $HOME needs to be set at some point during the configure phase
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(lambda _ (setenv "HOME" "/tmp")))
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(add-after 'unpack 'enter-dir
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(lambda _ (chdir "c++")))
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(add-after 'enter-dir 'fix-build-system
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(lambda _
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(define (which* cmd)
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(cond ((string=? cmd "date")
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;; make call to "date" deterministic
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"date -d @0")
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((which cmd)
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=> identity)
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(else
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(format (current-error-port)
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"WARNING: Unable to find absolute path for ~s~%"
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cmd)
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#false)))
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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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"src/build-system/Makefile.in.top"
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"src/build-system/Makefile.meta.gmake=no"
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"src/build-system/Makefile.meta.in"
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"src/build-system/Makefile.meta_l"
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"src/build-system/Makefile.meta_p"
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"src/build-system/Makefile.meta_r"
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"src/build-system/Makefile.mk.in"
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"src/build-system/Makefile.requirements"
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"src/build-system/Makefile.rules_with_autodep.in")
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(find-files "scripts/common/check" "\\.sh$"))
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(("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
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(or (which* cmd) all)))
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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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"src/build-system/Makefile.in.top"
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"src/build-system/Makefile.meta.gmake=no"
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"src/build-system/Makefile.meta.in"
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"src/build-system/Makefile.meta_l"
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"src/build-system/Makefile.meta_p"
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"src/build-system/Makefile.meta_r"
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"src/build-system/Makefile.mk.in"
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"src/build-system/Makefile.requirements"
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"src/build-system/Makefile.rules_with_autodep.in")
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(find-files "scripts/common/check" "\\.sh$"))
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(("(/usr/bin/|/bin/)([a-z][-_.a-z]*(\\+\\+)?)" all dir cmd)
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(or (which* cmd) all)))
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(substitute* (find-files "src/build-system" "^config.*")
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(("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
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(("^PATH=.*") ""))
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(substitute* (find-files "src/build-system" "^config.*")
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(("LN_S=/bin/\\$LN_S") (string-append "LN_S=" (which "ln")))
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(("^PATH=.*") ""))
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;; rewrite "/var/tmp" in check script
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(substitute* "scripts/common/check/check_make_unix.sh"
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(("/var/tmp") "/tmp"))
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;; rewrite "/var/tmp" in check script
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(substitute* "scripts/common/check/check_make_unix.sh"
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(("/var/tmp") "/tmp"))
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;; do not reset PATH
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(substitute* (find-files "scripts/common/impl/" "\\.sh$")
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(("^ *PATH=.*") "")
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(("action=/bin/") "action=")
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(("export PATH") ":"))
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#t))
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(replace 'configure
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(let ((out (assoc-ref outputs "out"))
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(lib (string-append (assoc-ref outputs "lib") "/lib"))
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(include (string-append (assoc-ref outputs "include")
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"/include/ncbi-tools++")))
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;; The 'configure' script doesn't recognize things like
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;; '--enable-fast-install'.
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(invoke "./configure.orig"
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(string-append "--with-build-root=" (getcwd) "/build")
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(string-append "--prefix=" out)
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(string-append "--libdir=" lib)
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(string-append "--includedir=" include)
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(string-append "--with-bz2="
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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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#t))))))
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;; do not reset PATH
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(substitute* (find-files "scripts/common/impl/" "\\.sh$")
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(("^ *PATH=.*") "")
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(("action=/bin/") "action=")
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(("export PATH") ":"))))
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(replace 'configure
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(lambda _
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(let ((lib (string-append #$output:lib "/lib"))
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(include (string-append #$output:include
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"/include/ncbi-tools++")))
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;; The 'configure' script doesn't recognize things like
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;; '--enable-fast-install'.
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(invoke "./configure.orig"
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(string-append "--with-build-root=" (getcwd) "/build")
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(string-append "--prefix=" #$output)
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(string-append "--libdir=" lib)
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(string-append "--includedir=" include)
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(string-append "--with-bz2="
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#$(this-package-input "bzip2"))
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(string-append "--with-z="
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#$(this-package-input "zlib"))
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(string-append "--with-pcre="
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#$(this-package-input "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" ; 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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("lmdb" ,lmdb)
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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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(list bzip2
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lmdb
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zlib
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pcre
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perl
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python-wrapper))
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(native-inputs
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(list cpio))
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(home-page "https://blast.ncbi.nlm.nih.gov")
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