gnu: salmon: Update to 1.4.0.
* gnu/packages/bioinformatics.scm (salmon): Update to 1.4.0. [arguments]: Remove unnecessary flags, add other soon-to-be-unnecessary flags; remove "prepare-rapmap" phase, add "prepare-pufferfish" phase, add "fix-error-message-in-tests" phase, simplify "use-system-libraries" phase. [inputs]: Add curl and pufferfish sources; remove libdivsufsort and rapmap sources.master
Ricardo Wurmus
parent
483cdf36a5
commit
bb38287570
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@ -9639,7 +9639,7 @@ 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 "0.13.1")
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(version "1.4.0")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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@ -9648,124 +9648,113 @@ 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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"1i2z4aivicmiixdz9bxalp7vmfzi3k92fxa63iqa8kgvfw5a4aq5"))
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"1di7y2s8cjr9480lngcmaz3wcabc1lpkyanzbhir1nkhcjmj70h4"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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;; Delete bundled headers for eigen3.
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(delete-file-recursively "include/eigen3/")
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#t))))
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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 "-DBOOST_INCLUDEDIR="
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(assoc-ref %build-inputs "boost")
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"/include/")
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(string-append "-DBOOST_LIBRARYDIR="
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(assoc-ref %build-inputs "boost")
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"/lib/")
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(string-append "-DBoost_LIBRARIES="
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"-lboost_iostreams "
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"-lboost_filesystem "
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"-lboost_system "
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"-lboost_thread "
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"-lboost_timer "
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"-lboost_chrono "
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"-lboost_program_options")
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"-DBoost_FOUND=TRUE"
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"-DTBB_LIBRARIES=tbb tbbmalloc"
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;; Don't download RapMap---we already have it!
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"-DFETCHED_RAPMAP=1")
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(list (string-append "-Dlibgff_DIR="
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(assoc-ref %build-inputs "libgff") "/lib")
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"-Dlibgff_FOUND=TRUE"
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"-DTBB_FOUND=TRUE"
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"-DTBB_VERSION=2020.3"
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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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#:phases
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(modify-phases %standard-phases
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;; Boost cannot be found, even though it's right there.
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(add-after 'unpack 'do-not-look-for-boost
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(add-after 'unpack 'prepare-pufferfish
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "CMakeLists.txt"
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(("find_package\\(Boost 1\\.59\\.0") "#"))
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#t))
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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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;; 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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#t))
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(add-after 'unpack 'prepare-rapmap
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((src "external/install/src/rapmap/")
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(include "external/install/include/rapmap/")
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(rapmap (assoc-ref inputs "rapmap")))
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(mkdir-p src)
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(mkdir-p include)
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(copy-recursively (string-append rapmap "/src") src)
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(copy-recursively (string-append rapmap "/include") include)
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(for-each delete-file '("external/install/include/rapmap/xxhash.h"
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"external/install/include/rapmap/FastxParser.hpp"
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"external/install/include/rapmap/concurrentqueue.h"
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"external/install/include/rapmap/FastxParserThreadUtils.hpp"
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"external/install/src/rapmap/FastxParser.cpp"
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"external/install/src/rapmap/xxhash.c"))
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(delete-file-recursively "external/install/include/rapmap/spdlog"))
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#t))
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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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(substitute* "CMakeLists.txt"
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;; Don't prefer static libs
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(("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
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(("set\\(TBB_LIBRARIES") "message(")
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;; Don't download anything
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(("DOWNLOAD_COMMAND") "DOWNLOAD_COMMAND echo")
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(("externalproject_add\\(libcereal") "message(")
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(("externalproject_add\\(libgff") "message(")
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(("externalproject_add\\(libtbb") "message(")
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(("externalproject_add\\(libdivsufsort") "message(")
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(("externalproject_add\\(libstadenio") "message(")
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(("externalproject_add_step\\(") "message("))
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(substitute* "src/CMakeLists.txt"
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(("add_dependencies") "#")
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(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libstaden-read.a")
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(string-append (assoc-ref inputs "libstadenio-for-salmon")
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"/lib/libstaden-read.so"))
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(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
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(string-append (assoc-ref inputs "libdivsufsort")
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"/lib/libdivsufsort.so"))
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(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
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(string-append (assoc-ref inputs "libdivsufsort")
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"/lib/libdivsufsort64.so"))
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(("lib/libdivsufsort.a") "/lib/libdivsufsort.so"))
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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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#t))
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;; CMAKE_INSTALL_PREFIX does not exist when the tests are
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;; run. It only exists after the install phase.
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(add-after 'unpack 'fix-tests
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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* "src/CMakeLists.txt"
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(("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
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"DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
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#t)))))
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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)
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("curl" ,curl)
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("eigen" ,eigen)
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("rapmap" ,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/COMBINE-lab/RapMap")
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(commit (string-append "salmon-v" version))))
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(file-name (string-append "rapmap-salmon-v" version "-checkout"))
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(sha256
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(base32
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"1biplxf0csc7a8h1wf219b0vmjkvw6wk2zylhdklb577kgmihdms"))))
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("jemalloc" ,jemalloc)
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("libgff" ,libgff)
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("pufferfish" ,(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/COMBINE-lab/pufferfish")
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(commit (string-append "salmon-v" version))))
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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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"0qb4a2nl1d59qasr17sslgxnkjd5kbk5mns4cjshrmsvkrqp995n"))))
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("tbb" ,tbb)
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("libdivsufsort" ,libdivsufsort)
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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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