gnu: Add sailfish.
* gnu/packages/bioinformatics.scm (sailfish): New variable.
This commit is contained in:
Ricardo Wurmus
parent
1fe0bde34d
commit
8d77a085a7
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@ -71,6 +71,7 @@
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#:use-module (gnu packages image)
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#:use-module (gnu packages imagemagick)
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#:use-module (gnu packages java)
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#:use-module (gnu packages jemalloc)
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#:use-module (gnu packages ldc)
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#:use-module (gnu packages linux)
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#:use-module (gnu packages logging)
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@ -11160,3 +11161,149 @@ Burrows-Wheeler transformed string from a given string over a constant-size
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alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
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bytes of memory space, where n is the length of the string.")
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(license license:expat)))
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(define-public sailfish
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(package
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(name "sailfish")
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(version "0.10.1")
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(source (origin
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(method url-fetch)
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(uri
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(string-append "https://github.com/kingsfordgroup/"
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"sailfish/archive/v" version ".tar.gz"))
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(file-name (string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
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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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;; Don't download RapMap---we already have it!
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"-DFETCHED_RAPMAP=1")
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;; Tests must be run after installation and the location of the test
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;; data file must be overridden. But the tests fail. It looks like
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;; they are not really meant to be run.
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#:tests? #f
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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-assign-to-macro
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(lambda _
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(substitute* "include/spdlog/details/format.cc"
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(("const unsigned CHAR_WIDTH = 1;") ""))))
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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 "/tmp/rapmap")
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(system* "tar" "xf"
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(assoc-ref inputs "rapmap")
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"-C" "/tmp/rapmap"
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"--strip-components=1")
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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 "/tmp/rapmap/src" "\\.(c|cpp)"))
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(copy-recursively "/tmp/rapmap/include" include))))
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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/SailfishIndexer.cpp"
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"src/SailfishUtils.cpp"
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"src/SailfishQuantify.cpp"
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"src/FASTAParser.cpp"
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"include/PCA.hpp"
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"include/SailfishUtils.hpp"
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"include/SailfishIndex.hpp"
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"include/CollapsedEMOptimizer.hpp"
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"src/CollapsedEMOptimizer.cpp")
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(("#include \"jellyfish/config.h\"") ""))
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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/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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(("find_package\\(Jellyfish.*") "")
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(("ExternalProject_Add\\(libjellyfish") "message(")
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(("ExternalProject_Add\\(libgff") "message(")
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(("ExternalProject_Add\\(libsparsehash") "message(")
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(("ExternalProject_Add\\(libdivsufsort") "message("))
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;; Ensure that Eigen 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 "eigen")
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"/include/eigen3")))))))
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(inputs
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`(("boost" ,boost)
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("eigen" ,eigen)
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("jemalloc" ,jemalloc)
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("jellyfish" ,jellyfish)
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("sparsehash" ,sparsehash)
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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 "sf-v" version))))
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(file-name (string-append "rapmap-sf-v" version "-checkout"))
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(sha256
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(base32
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"1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
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(modules '((guix build utils)))
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;; These files are expected to be excluded.
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(snippet
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'(begin (delete-file-recursively "include/spdlog")
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(for-each delete-file '("include/xxhash.h"
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"src/xxhash.c"))))))
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("libdivsufsort" ,libdivsufsort)
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("libgff" ,libgff)
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("tbb" ,tbb)
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("zlib" ,zlib)))
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(native-inputs
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`(("pkg-config" ,pkg-config)))
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(home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
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(synopsis "Mapping-based isoform quantification from RNA-Seq reads")
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(description "Sailfish is a tool for genomic transcript quantification
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from RNA-seq data. It requires a set of target transcripts (either from a
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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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