@@ 71,6 71,7 @@
#:use-module (gnu packages image)
#:use-module (gnu packages imagemagick)
#:use-module (gnu packages java)
+ #:use-module (gnu packages jemalloc)
#:use-module (gnu packages ldc)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
@@ 11160,3 11161,149 @@ Burrows-Wheeler transformed string from a given string over a constant-size
alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1)
bytes of memory space, where n is the length of the string.")
(license license:expat)))
+
+(define-public sailfish
+ (package
+ (name "sailfish")
+ (version "0.10.1")
+ (source (origin
+ (method url-fetch)
+ (uri
+ (string-append "https://github.com/kingsfordgroup/"
+ "sailfish/archive/v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1inn60dxiwsz8g9w7kvfhjxj4bwfb0r12dyhpzzhfbig712dkmm0"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete bundled headers for eigen3.
+ (delete-file-recursively "include/eigen3/")
+ #t))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags
+ (list (string-append "-DBOOST_INCLUDEDIR="
+ (assoc-ref %build-inputs "boost")
+ "/include/")
+ (string-append "-DBOOST_LIBRARYDIR="
+ (assoc-ref %build-inputs "boost")
+ "/lib/")
+ (string-append "-DBoost_LIBRARIES="
+ "-lboost_iostreams "
+ "-lboost_filesystem "
+ "-lboost_system "
+ "-lboost_thread "
+ "-lboost_timer "
+ "-lboost_chrono "
+ "-lboost_program_options")
+ "-DBoost_FOUND=TRUE"
+ ;; Don't download RapMap---we already have it!
+ "-DFETCHED_RAPMAP=1")
+ ;; Tests must be run after installation and the location of the test
+ ;; data file must be overridden. But the tests fail. It looks like
+ ;; they are not really meant to be run.
+ #:tests? #f
+ #:phases
+ (modify-phases %standard-phases
+ ;; Boost cannot be found, even though it's right there.
+ (add-after 'unpack 'do-not-look-for-boost
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "CMakeLists.txt"
+ (("find_package\\(Boost 1\\.53\\.0") "#"))))
+ (add-after 'unpack 'do-not-assign-to-macro
+ (lambda _
+ (substitute* "include/spdlog/details/format.cc"
+ (("const unsigned CHAR_WIDTH = 1;") ""))))
+ (add-after 'unpack 'prepare-rapmap
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((src "external/install/src/rapmap/")
+ (include "external/install/include/rapmap/")
+ (rapmap (assoc-ref inputs "rapmap")))
+ (mkdir-p "/tmp/rapmap")
+ (system* "tar" "xf"
+ (assoc-ref inputs "rapmap")
+ "-C" "/tmp/rapmap"
+ "--strip-components=1")
+ (mkdir-p src)
+ (mkdir-p include)
+ (for-each (lambda (file)
+ (install-file file src))
+ (find-files "/tmp/rapmap/src" "\\.(c|cpp)"))
+ (copy-recursively "/tmp/rapmap/include" include))))
+ (add-after 'unpack 'use-system-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* '("src/SailfishIndexer.cpp"
+ "src/SailfishUtils.cpp"
+ "src/SailfishQuantify.cpp"
+ "src/FASTAParser.cpp"
+ "include/PCA.hpp"
+ "include/SailfishUtils.hpp"
+ "include/SailfishIndex.hpp"
+ "include/CollapsedEMOptimizer.hpp"
+ "src/CollapsedEMOptimizer.cpp")
+ (("#include \"jellyfish/config.h\"") ""))
+ (substitute* "src/CMakeLists.txt"
+ (("\\$\\{GAT_SOURCE_DIR\\}/external/install/include/jellyfish-2.2..")
+ (string-append (assoc-ref inputs "jellyfish")
+ "/include/jellyfish-" ,(package-version jellyfish)))
+ (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libjellyfish-2.0.a")
+ (string-append (assoc-ref inputs "jellyfish")
+ "/lib/libjellyfish-2.0.a"))
+ (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort.a")
+ (string-append (assoc-ref inputs "libdivsufsort")
+ "/lib/libdivsufsort.so"))
+ (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libdivsufsort64.a")
+ (string-append (assoc-ref inputs "libdivsufsort")
+ "/lib/libdivsufsort64.so")))
+ (substitute* "CMakeLists.txt"
+ ;; Don't prefer static libs
+ (("SET\\(CMAKE_FIND_LIBRARY_SUFFIXES.*") "")
+ (("find_package\\(Jellyfish.*") "")
+ (("ExternalProject_Add\\(libjellyfish") "message(")
+ (("ExternalProject_Add\\(libgff") "message(")
+ (("ExternalProject_Add\\(libsparsehash") "message(")
+ (("ExternalProject_Add\\(libdivsufsort") "message("))
+
+ ;; Ensure that Eigen headers can be found
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (getenv "CPLUS_INCLUDE_PATH")
+ ":"
+ (assoc-ref inputs "eigen")
+ "/include/eigen3")))))))
+ (inputs
+ `(("boost" ,boost)
+ ("eigen" ,eigen)
+ ("jemalloc" ,jemalloc)
+ ("jellyfish" ,jellyfish)
+ ("sparsehash" ,sparsehash)
+ ("rapmap" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/RapMap.git")
+ (commit (string-append "sf-v" version))))
+ (file-name (string-append "rapmap-sf-v" version "-checkout"))
+ (sha256
+ (base32
+ "1hv79l5i576ykv5a1srj2p0q36yvyl5966m0fcy2lbi169ipjakf"))
+ (modules '((guix build utils)))
+ ;; These files are expected to be excluded.
+ (snippet
+ '(begin (delete-file-recursively "include/spdlog")
+ (for-each delete-file '("include/xxhash.h"
+ "src/xxhash.c"))))))
+ ("libdivsufsort" ,libdivsufsort)
+ ("libgff" ,libgff)
+ ("tbb" ,tbb)
+ ("zlib" ,zlib)))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (home-page "http://www.cs.cmu.edu/~ckingsf/software/sailfish")
+ (synopsis "Mapping-based isoform quantification from RNA-Seq reads")
+ (description "Sailfish is a tool for genomic transcript quantification
+from RNA-seq data. It requires a set of target transcripts (either from a
+reference or de-novo assembly) to quantify. All you need to run sailfish is a
+fasta file containing your reference transcripts and a (set of) fasta/fastq
+file(s) containing your reads.")
+ (license license:gpl3+)))