gnu: ncbi-vdb: Ensure that vdb-sqlite is installed.
The most important change here is the addition of the 'install-libs phase. All other changes are just the result of switching to G-expressions. * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Add 'install-libs phase; use G-expression; drop trailing #T from build phases. [inputs]: Drop package labels.
This commit is contained in:
Ricardo Wurmus
parent
263f235cd0
commit
8ba3bf6564
@ -7561,99 +7561,99 @@ simultaneously.")
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"0m8hlxscidsfqm9x9fyi62q6lpf1dv5115kgjjgnrkl49q9c27m6"))))
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(build-system gnu-build-system)
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(arguments
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`(#:parallel-build? #f ; not supported
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#:tests? #f ; no "check" target
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#:make-flags '("HAVE_HDF5=1")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'make-files-writable
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(lambda _ (for-each make-file-writable (find-files "." ".*")) #t))
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(add-before 'configure 'set-perl-search-path
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(lambda _
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;; Work around "dotless @INC" build failure.
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(setenv "PERL5LIB"
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(string-append (getcwd) "/setup:"
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(getenv "PERL5LIB")))
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#t))
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;; See https://github.com/ncbi/ncbi-vdb/issues/14
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(add-after 'unpack 'patch-krypto-flags
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(lambda _
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(substitute* "libs/krypto/Makefile"
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(("-Wa,-march=generic64\\+aes") "")
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(("-Wa,-march=generic64\\+sse4") ""))
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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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;; Override include path for libmagic
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(substitute* "setup/package.prl"
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(("name => 'magic', Include => '/usr/include'")
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(string-append "name=> 'magic', Include => '"
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(assoc-ref inputs "libmagic")
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"/include" "'")))
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(list
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#:parallel-build? #f ; not supported
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#:tests? #f ; no "check" target
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#:make-flags '(list "HAVE_HDF5=1")
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#:phases
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#~(modify-phases %standard-phases
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#;
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(add-after 'unpack 'make-files-writable
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(lambda _ (for-each make-file-writable (find-files "." ".*"))))
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(add-before 'configure 'set-perl-search-path
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(lambda _
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;; Work around "dotless @INC" build failure.
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(setenv "PERL5LIB"
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(string-append (getcwd) "/setup:"
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(getenv "PERL5LIB")))))
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;; See https://github.com/ncbi/ncbi-vdb/issues/14
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(add-after 'unpack 'patch-krypto-flags
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(lambda _
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(substitute* "libs/krypto/Makefile"
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(("-Wa,-march=generic64\\+aes") "")
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(("-Wa,-march=generic64\\+sse4") ""))))
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(replace 'configure
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(lambda _
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;; Override include path for libmagic
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(substitute* "setup/package.prl"
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(("name => 'magic', Include => '/usr/include'")
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(string-append "name=> 'magic', Include => '"
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#$(this-package-input "file")
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"/include" "'")))
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;; Install kdf5 library (needed by sra-tools)
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(substitute* "build/Makefile.install"
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(("LIBRARIES_TO_INSTALL =")
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"LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
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;; Install kdf5 library (needed by sra-tools)
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(substitute* "build/Makefile.install"
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(("LIBRARIES_TO_INSTALL =")
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"LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)"))
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(substitute* "build/Makefile.env"
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(("CFLAGS =" prefix)
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(string-append prefix "-msse2 ")))
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(substitute* "build/Makefile.env"
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(("CFLAGS =" prefix)
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(string-append prefix "-msse2 ")))
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;; Override search path for ngs-java
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(substitute* "setup/package.prl"
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(("/usr/local/ngs/ngs-java")
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(assoc-ref inputs "java-ngs")))
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;; Override search path for ngs-java
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(substitute* "setup/package.prl"
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(("/usr/local/ngs/ngs-java")
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#$(this-package-input "java-ngs")))
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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"
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(string-append "--build-prefix=" (getcwd) "/build")
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(string-append "--prefix=" (assoc-ref outputs "out"))
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(string-append "--debug")
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(string-append "--with-xml2-prefix="
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(assoc-ref inputs "libxml2"))
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(string-append "--with-ngs-sdk-prefix="
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(assoc-ref inputs "ngs-sdk"))
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(string-append "--with-hdf5-prefix="
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(assoc-ref inputs "hdf5")))
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#t)))
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(add-after 'install 'install-interfaces
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(lambda* (#:key outputs #:allow-other-keys)
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;; Install interface libraries. On i686 the interface libraries
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;; are installed to "linux/gcc/i386", so we need to use the Linux
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;; architecture name ("i386") instead of the target system prefix
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;; ("i686").
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(mkdir (string-append (assoc-ref outputs "out") "/ilib"))
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(copy-recursively (string-append
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"build/ncbi-vdb/linux/gcc/"
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,(platform-linux-architecture
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(lookup-platform-by-target-or-system
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(or (%current-target-system)
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(%current-system))))
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"/rel/ilib")
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(string-append (assoc-ref outputs "out")
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"/ilib"))
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;; Install interface headers
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(copy-recursively "interfaces"
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(string-append (assoc-ref outputs "out")
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"/include"))
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#t))
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;; These files are needed by sra-tools.
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(add-after 'install 'install-configuration-files
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(lambda* (#:key outputs #:allow-other-keys)
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(let ((target (string-append (assoc-ref outputs "out") "/kfg")))
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(mkdir target)
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(install-file "libs/kfg/default.kfg" target)
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(install-file "libs/kfg/certs.kfg" target))
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#t)))))
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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"
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(string-append "--build-prefix=" (getcwd) "/build")
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(string-append "--prefix=" #$output)
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(string-append "--debug")
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(string-append "--with-xml2-prefix="
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#$(this-package-input "libxml2"))
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(string-append "--with-ngs-sdk-prefix="
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#$(this-package-input "ngs-sdk"))
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(string-append "--with-hdf5-prefix="
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#$(this-package-input "hdf5")))))
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(add-after 'install 'install-interfaces
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(lambda _
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;; Install interface libraries. On i686 the interface libraries
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;; are installed to "linux/gcc/i386", so we need to use the Linux
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;; architecture name ("i386") instead of the target system prefix
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;; ("i686").
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(mkdir (string-append #$output "/ilib"))
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(copy-recursively (string-append
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"build/ncbi-vdb/linux/gcc/"
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#$(platform-linux-architecture
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(lookup-platform-by-target-or-system
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(or (%current-target-system)
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(%current-system))))
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"/rel/ilib")
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(string-append #$output "/ilib"))
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;; Install interface headers
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(copy-recursively "interfaces"
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(string-append #$output "/include"))))
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(add-after 'install-interfaces 'install-libs
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(lambda _
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(copy-recursively (string-append
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"build/ncbi-vdb/linux/gcc/"
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#$(platform-linux-architecture
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(lookup-platform-by-target-or-system
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(or (%current-target-system)
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(%current-system))))
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"/rel/lib")
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(string-append #$output "/lib"))))
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;; These files are needed by sra-tools.
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(add-after 'install 'install-configuration-files
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(lambda _
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(let ((target (string-append #$output "/kfg")))
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(mkdir target)
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(install-file "libs/kfg/default.kfg" target)
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(install-file "libs/kfg/certs.kfg" target)))))))
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(inputs
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`(("libxml2" ,libxml2)
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("ngs-sdk" ,ngs-sdk)
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("java-ngs" ,java-ngs)
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("libmagic" ,file)
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("hdf5" ,hdf5)))
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(list file hdf5 java-ngs libxml2 ngs-sdk ))
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(native-inputs (list perl))
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;; NCBI-VDB requires SSE capability.
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(supported-systems '("i686-linux" "x86_64-linux"))
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