gnu: Add salmon.
* gnu/packages/bioinformatics.scm (libstadenio-for-salmon, spdlog-for-salmon, bwa-for-salmon, salmon): New variables.
This commit is contained in:
Ricardo Wurmus
parent
8d77a085a7
commit
7762646d95
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@ -11307,3 +11307,266 @@ reference or de-novo assembly) to quantify. All you need to run sailfish is a
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fasta file containing your reference transcripts and a (set of) fasta/fastq
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file(s) containing your reads.")
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(license license:gpl3+)))
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(define libstadenio-for-salmon
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(package
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(name "libstadenio")
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(version "1.14.8")
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(source (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/staden-io_lib.git")
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(commit (string-append "v" version))))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
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(build-system gnu-build-system)
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(arguments '(#:parallel-tests? #f)) ; not supported
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(inputs
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`(("zlib" ,zlib)))
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(native-inputs
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`(("perl" ,perl))) ; for tests
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(home-page "https://github.com/COMBINE-lab/staden-io_lib")
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(synopsis "General purpose trace and experiment file library")
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(description "This package provides a library of file reading and writing
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code to provide a general purpose Trace file (and Experiment File) reading
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interface.
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The following file formats are supported:
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@enumerate
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@item SCF trace files
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@item ABI trace files
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@item ALF trace files
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@item ZTR trace files
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@item SFF trace archives
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@item SRF trace archives
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@item Experiment files
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@item Plain text files
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@item SAM/BAM sequence files
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@item CRAM sequence files
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@end enumerate\n")
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(license license:bsd-3)))
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(define spdlog-for-salmon
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(package
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(name "spdlog")
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(version "0.14.0")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/COMBINE-lab/spdlog.git")
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(commit (string-append "v" version))))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
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(build-system cmake-build-system)
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(home-page "https://github.com/COMBINE-lab/spdlog")
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(synopsis "Very fast C++ logging library")
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(description "Spdlog is a very fast header-only C++ logging library with
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performance as its primary goal.")
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(license license:expat)))
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;; This is a modified variant of bwa for use with Salmon. It installs a
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;; library to avoid having to build this as part of Salmon.
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(define bwa-for-salmon
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(package (inherit bwa)
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(name "bwa")
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(version "0.7.12.5")
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(source (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/bwa.git")
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(commit (string-append "v" version))))
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(file-name (string-append "bwa-for-salmon-" version "-checkout"))
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(sha256
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(base32
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"1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
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(build-system gnu-build-system)
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(arguments
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'(#:tests? #f ;no "check" target
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#:phases
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(modify-phases %standard-phases
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(replace 'install
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(lambda* (#:key outputs #:allow-other-keys)
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(let* ((out (assoc-ref outputs "out"))
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(bin (string-append out "/bin"))
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(lib (string-append out "/lib"))
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(doc (string-append out "/share/doc/bwa"))
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(man (string-append out "/share/man/man1"))
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(inc (string-append out "/include/bwa")))
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(install-file "bwa" bin)
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(install-file "README.md" doc)
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(install-file "bwa.1" man)
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(install-file "libbwa.a" lib)
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(mkdir-p lib)
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(mkdir-p inc)
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(for-each (lambda (file)
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(install-file file inc))
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(find-files "." "\\.h$")))
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#t))
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;; no "configure" script
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(delete 'configure))))))
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(define-public salmon
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(package
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(name "salmon")
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(version "0.9.1")
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(source (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/salmon.git")
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(commit (string-append "v" version))))
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(file-name (string-append name "-" version "-checkout"))
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(sha256
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(base32
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"1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
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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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(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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#: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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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "CMakeLists.txt"
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(("find_package\\(Boost 1\\.53\\.0") "#"))))
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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 '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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(for-each (lambda (file)
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(install-file file src))
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(find-files (string-append rapmap "/src") "\\.(c|cpp)"))
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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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(add-after 'unpack 'use-system-libraries
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(lambda* (#:key inputs #:allow-other-keys)
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(substitute* "src/CMakeLists.txt"
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(("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
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(string-append (assoc-ref inputs "jellyfish")
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"/include/jellyfish-" ,(package-version jellyfish)))
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(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
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(string-append (assoc-ref inputs "jellyfish")
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"/lib/libjellyfish-2.0.a"))
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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/libstaden-read.a")
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(string-append (assoc-ref inputs "libstadenio-for-salmon")
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"/lib/libstaden-read.a"))
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(("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
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(string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
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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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(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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(("find_package\\(Jellyfish.*") "")
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(("ExternalProject_Add\\(libcereal") "message(")
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(("ExternalProject_Add\\(libbwa") "message(")
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(("ExternalProject_Add\\(libjellyfish") "message(")
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(("ExternalProject_Add\\(libgff") "message(")
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(("ExternalProject_Add\\(libtbb") "message(")
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(("ExternalProject_Add\\(libspdlog") "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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;; Ensure that all headers can be found
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(setenv "CPLUS_INCLUDE_PATH"
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(string-append (getenv "CPLUS_INCLUDE_PATH")
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":"
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(assoc-ref inputs "bwa")
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"/include/bwa"
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":"
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(assoc-ref inputs "eigen")
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"/include/eigen3"))
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(setenv "CPATH"
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(string-append (assoc-ref inputs "bwa")
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"/include/bwa"
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":"
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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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(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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(inputs
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`(("boost" ,boost)
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("bwa" ,bwa-for-salmon)
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("bzip2" ,bzip2)
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("cereal" ,cereal)
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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.git")
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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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"1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
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("jemalloc" ,jemalloc)
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("jellyfish" ,jellyfish)
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("libgff" ,libgff)
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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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("spdlog-for-salmon" ,spdlog-for-salmon)
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("xz" ,xz)
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("zlib" ,zlib)))
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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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transcript-level quantification estimates from RNA-seq data. Salmon achieves
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its accuracy and speed via a number of different innovations, including the
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use of lightweight alignments (accurate but fast-to-compute proxies for
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traditional read alignments) and massively-parallel stochastic collapsed
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variational inference.")
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(license license:gpl3+)))
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