gnu: salmon: Update to 1.9.0.
* gnu/packages/bioinformatics.scm (salmon): Update to 1.9.0. [arguments]: Remove -DTBB_LIBRARIES from configure flags; copy pufferfish itlib headers. [inputs]: Use new label-less list; move pufferfish origin from here... [native-inputs]: ...to here.master
Ricardo Wurmus
parent
729ce5fcf8
commit
1266b9ed11
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@ -10296,7 +10296,7 @@ The following file formats are supported:
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(define-public salmon
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(package
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(name "salmon")
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(version "1.6.0")
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(version "1.9.0")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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@ -10305,104 +10305,112 @@ The following file formats are supported:
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1wb5wl0rc77svbwq6zvak5h7pf9acw3di0vz5i3gqyhg5l6qd736"))
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"1370ry3jpj05gplzyny44mqg77a29a6gp8ijmjz135d2igf956r8"))
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(modules '((guix build utils)))
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(snippet
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;; Delete bundled headers for eigen3.
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'(delete-file-recursively "include/eigen3/"))))
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(build-system cmake-build-system)
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(arguments
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`(#:configure-flags
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,#~(list (string-append "-Dlibgff_DIR="
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#$(this-package-input "libgff") "/lib")
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"-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\""
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"-Dlibgff_FOUND=TRUE"
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"-DTBB_FOUND=TRUE"
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#$(string-append "-DTBB_VERSION=" (package-version tbb-2020))
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"-DTBB_LIBRARIES=tbb -ltbbmalloc"
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"-DFETCHED_PUFFERFISH=TRUE"
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"-DUSE_SHARED_LIBS=TRUE")
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(list
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#:configure-flags
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#~(list (string-append "-Dlibgff_DIR="
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#$(this-package-input "libgff") "/lib")
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"-DCMAKE_CXX_FLAGS=\"-DHAVE_NUMERIC_LIMITS128=1\""
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"-Dlibgff_FOUND=TRUE"
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"-DTBB_FOUND=TRUE"
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#$(string-append "-DTBB_VERSION=" (package-version tbb))
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"-DFETCHED_PUFFERFISH=TRUE"
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"-DUSE_SHARED_LIBS=TRUE")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'prepare-pufferfish
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(lambda* (#:key inputs #:allow-other-keys)
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(copy-recursively (assoc-ref inputs "pufferfish")
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"external/pufferfish")
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;; This test isn't working correctly, so compilation aborts.
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(substitute* "external/pufferfish/include/string_view.hpp"
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(("#if __has_include\\(<string_view>\\)")
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"#if 0"))
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(let ((headers "external/install/pufferfish/include/pufferfish")
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(source "external/install/src/pufferfish"))
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(mkdir-p headers)
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(mkdir-p source)
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(for-each (lambda (file)
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(install-file (string-append "external/pufferfish/include/" file)
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headers))
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(list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp"
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"Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp"
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"CanonicalKmerIterator.hpp"
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"PufferfishBaseIndex.hpp"
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"PufferfishIndex.hpp"
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"PufferfishSparseIndex.hpp"
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"PufferfishLossyIndex.hpp"
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"PufferfishTypes.hpp"
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"rank9b.hpp" "rank9sel.hpp" "macros.hpp"
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"select.hpp" "Util.hpp"
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"PairedAlignmentFormatter.hpp"
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"SelectiveAlignmentUtils.hpp"
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"PuffAligner.hpp" "MemCollector.hpp"
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"MemChainer.hpp" "CommonTypes.hpp"
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"SAMWriter.hpp" "PufferfishConfig.hpp"
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"BulkChunk.hpp" "BinWriter.hpp"))
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(for-each (lambda (dir)
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(copy-recursively
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(string-append "external/pufferfish/include/" dir)
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(string-append headers "/" dir)))
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(list "libdivide"
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"ksw2pp"
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"compact_vector"
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"metro"
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"chobo"
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"sparsepp"
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"simde"
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"tsl"))
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(copy-recursively
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(string-append "external/pufferfish/src/metro/")
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(string-append source "/metro"))
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(install-file
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(string-append "external/pufferfish/src/rank9b.cpp")
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source)
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'(modify-phases %standard-phases
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(add-after 'unpack 'prepare-pufferfish
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(lambda* (#:key inputs #:allow-other-keys)
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(copy-recursively (assoc-ref inputs "pufferfish")
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"external/pufferfish")
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;; This test isn't working correctly, so compilation aborts.
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(substitute* "external/pufferfish/include/string_view.hpp"
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(("#if __has_include\\(<string_view>\\)")
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"#if 0"))
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(let ((headers "external/install/pufferfish/include/pufferfish")
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(source "external/install/src/pufferfish"))
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(mkdir-p headers)
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(mkdir-p source)
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(for-each (lambda (file)
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(install-file (string-append "external/pufferfish/include/" file)
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headers))
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(list "ProgOpts.hpp" "BooPHF.hpp" "SpinLock.hpp"
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"Kmer.hpp" "CanonicalKmer.hpp" "string_view.hpp"
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"CanonicalKmerIterator.hpp"
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"PufferfishBaseIndex.hpp"
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"PufferfishIndex.hpp"
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"PufferfishSparseIndex.hpp"
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"PufferfishLossyIndex.hpp"
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"PufferfishTypes.hpp"
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"rank9b.hpp" "rank9sel.hpp" "macros.hpp"
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"select.hpp" "Util.hpp"
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"PairedAlignmentFormatter.hpp"
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"SelectiveAlignmentUtils.hpp"
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"PuffAligner.hpp" "MemCollector.hpp"
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"MemChainer.hpp" "CommonTypes.hpp"
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"SAMWriter.hpp" "PufferfishConfig.hpp"
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"BulkChunk.hpp" "BinWriter.hpp"))
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;; Do not complain about not having built libtbb
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(substitute* "external/pufferfish/external/twopaco/CMakeLists.txt"
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(("add_dependencies.*") "")))))
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(add-after 'unpack 'do-not-phone-home
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(lambda _
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(substitute* "src/Salmon.cpp"
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(("getVersionMessage\\(\\)") "\"\""))))
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(add-after 'unpack 'use-system-libraries
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(lambda* (#:key inputs #:allow-other-keys)
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;; Ensure that all headers can be found
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(setenv "CPLUS_INCLUDE_PATH"
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(string-append (or (getenv "CPLUS_INCLUDE_PATH") "")
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":"
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(getcwd) "/external/install/pufferfish/include:"
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(assoc-ref inputs "eigen")
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"/include/eigen3"))))
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(add-after 'unpack 'fix-error-message-in-tests
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(lambda _
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(substitute* "cmake/TestSalmonQuasi.cmake"
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(("SALMON_QUASI_INDEX_COMMAND")
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"SALMON_QUASI_INDEX_CMD")))))))
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(for-each (lambda (dir)
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(copy-recursively
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(string-append "external/pufferfish/include/" dir)
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(string-append headers "/" dir)))
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(list "libdivide"
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"ksw2pp"
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"compact_vector"
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"itlib"
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"metro"
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"chobo"
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"sparsepp"
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"simde"
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"tsl"))
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(copy-recursively
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(string-append "external/pufferfish/src/metro/")
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(string-append source "/metro"))
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(install-file
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(string-append "external/pufferfish/src/rank9b.cpp")
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source)
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;; Do not complain about not having built libtbb
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(substitute* "external/pufferfish/external/twopaco/CMakeLists.txt"
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(("add_dependencies.*") "")))))
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(add-after 'unpack 'do-not-phone-home
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(lambda _
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(substitute* "src/Salmon.cpp"
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(("getVersionMessage\\(\\)") "\"\""))))
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(add-after 'unpack 'use-system-libraries
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(lambda* (#:key inputs #:allow-other-keys)
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;; Ensure that all headers can be found
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(setenv "CPLUS_INCLUDE_PATH"
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(string-append (or (getenv "CPLUS_INCLUDE_PATH") "")
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":"
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(getcwd) "/external/install/pufferfish/include:"
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(assoc-ref inputs "eigen")
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"/include/eigen3"))))
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(add-after 'unpack 'fix-error-message-in-tests
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(lambda _
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(substitute* "cmake/TestSalmonQuasi.cmake"
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(("SALMON_QUASI_INDEX_COMMAND")
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"SALMON_QUASI_INDEX_CMD")))))))
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(inputs
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`(("boost" ,boost)
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("bzip2" ,bzip2)
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("cereal" ,cereal-1.3.0)
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("curl" ,curl)
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("eigen" ,eigen)
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("jemalloc" ,jemalloc)
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("libgff" ,libgff)
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(list boost
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bzip2
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cereal-1.3.0
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curl
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eigen
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jemalloc
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libgff
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tbb
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libstadenio-for-salmon
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xz
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zlib))
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(native-inputs
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`(("pkg-config" ,pkg-config)
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("pufferfish" ,(origin
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(method git-fetch)
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(uri (git-reference
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@ -10411,13 +10419,7 @@ The following file formats are supported:
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(file-name (git-file-name "pufferfish" version))
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(sha256
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(base32
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"0jakgpbanl6cs23x3g26iab54p7zylcf9v8vc32ps57smp8wql52"))))
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("tbb" ,tbb-2020)
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("libstadenio-for-salmon" ,libstadenio-for-salmon)
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("xz" ,xz)
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("zlib" ,zlib)))
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(native-inputs
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(list pkg-config))
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"048a006mc2d0h78ym58mv67hl1pj480ilc5ifq0rlzfdyyfs1b8i"))))))
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(home-page "https://github.com/COMBINE-lab/salmon")
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(synopsis "Quantification from RNA-seq reads using lightweight alignments")
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(description "Salmon is a program to produce highly-accurate,
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