@@ 11307,3 11307,266 @@ 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+)))
+
+(define libstadenio-for-salmon
+ (package
+ (name "libstadenio")
+ (version "1.14.8")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/staden-io_lib.git")
+ (commit (string-append "v" version))))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1x8kxxqxl892vwfbprlbyfwkkv7c34ggkc94892x9x0g37x5nbwx"))))
+ (build-system gnu-build-system)
+ (arguments '(#:parallel-tests? #f)) ; not supported
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("perl" ,perl))) ; for tests
+ (home-page "https://github.com/COMBINE-lab/staden-io_lib")
+ (synopsis "General purpose trace and experiment file library")
+ (description "This package provides a library of file reading and writing
+code to provide a general purpose Trace file (and Experiment File) reading
+interface.
+
+The following file formats are supported:
+
+@enumerate
+@item SCF trace files
+@item ABI trace files
+@item ALF trace files
+@item ZTR trace files
+@item SFF trace archives
+@item SRF trace archives
+@item Experiment files
+@item Plain text files
+@item SAM/BAM sequence files
+@item CRAM sequence files
+@end enumerate\n")
+ (license license:bsd-3)))
+
+(define spdlog-for-salmon
+ (package
+ (name "spdlog")
+ (version "0.14.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/spdlog.git")
+ (commit (string-append "v" version))))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "13730429gwlabi432ilpnja3sfvy0nn2719vnhhmii34xcdyc57q"))))
+ (build-system cmake-build-system)
+ (home-page "https://github.com/COMBINE-lab/spdlog")
+ (synopsis "Very fast C++ logging library")
+ (description "Spdlog is a very fast header-only C++ logging library with
+performance as its primary goal.")
+ (license license:expat)))
+
+;; This is a modified variant of bwa for use with Salmon. It installs a
+;; library to avoid having to build this as part of Salmon.
+(define bwa-for-salmon
+ (package (inherit bwa)
+ (name "bwa")
+ (version "0.7.12.5")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/bwa.git")
+ (commit (string-append "v" version))))
+ (file-name (string-append "bwa-for-salmon-" version "-checkout"))
+ (sha256
+ (base32
+ "1z2qa64y0c5hky10510x137mnzlhz6k8qf27csw4w9j6qihq95gb"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ (doc (string-append out "/share/doc/bwa"))
+ (man (string-append out "/share/man/man1"))
+ (inc (string-append out "/include/bwa")))
+ (install-file "bwa" bin)
+ (install-file "README.md" doc)
+ (install-file "bwa.1" man)
+ (install-file "libbwa.a" lib)
+ (mkdir-p lib)
+ (mkdir-p inc)
+ (for-each (lambda (file)
+ (install-file file inc))
+ (find-files "." "\\.h$")))
+ #t))
+ ;; no "configure" script
+ (delete 'configure))))))
+
+(define-public salmon
+ (package
+ (name "salmon")
+ (version "0.9.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/salmon.git")
+ (commit (string-append "v" version))))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1zi1ff4i7y2ykk0vdzysgwzzzv166vg2x77pj1mf4baclavxj87a"))
+ (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"
+ "-DTBB_LIBRARIES=tbb tbbmalloc"
+ ;; Don't download RapMap---we already have it!
+ "-DFETCHED_RAPMAP=1")
+ #: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-phone-home
+ (lambda _
+ (substitute* "src/Salmon.cpp"
+ (("getVersionMessage\\(\\)") "\"\""))))
+ (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 src)
+ (mkdir-p include)
+ (for-each (lambda (file)
+ (install-file file src))
+ (find-files (string-append rapmap "/src") "\\.(c|cpp)"))
+ (copy-recursively (string-append rapmap "/include") include)
+ (for-each delete-file '("external/install/include/rapmap/xxhash.h"
+ "external/install/include/rapmap/FastxParser.hpp"
+ "external/install/include/rapmap/concurrentqueue.h"
+ "external/install/include/rapmap/FastxParserThreadUtils.hpp"
+ "external/install/src/rapmap/FastxParser.cpp"
+ "external/install/src/rapmap/xxhash.c")))))
+ (add-after 'unpack 'use-system-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (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/libstaden-read.a")
+ (string-append (assoc-ref inputs "libstadenio-for-salmon")
+ "/lib/libstaden-read.a"))
+ (("\\$\\{GAT_SOURCE_DIR\\}/external/install/lib/libbwa.a")
+ (string-append (assoc-ref inputs "bwa") "/lib/libbwa.a"))
+ (("\\$\\{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.*") "")
+ (("set\\(TBB_LIBRARIES") "message(")
+ (("find_package\\(Jellyfish.*") "")
+ (("ExternalProject_Add\\(libcereal") "message(")
+ (("ExternalProject_Add\\(libbwa") "message(")
+ (("ExternalProject_Add\\(libjellyfish") "message(")
+ (("ExternalProject_Add\\(libgff") "message(")
+ (("ExternalProject_Add\\(libtbb") "message(")
+ (("ExternalProject_Add\\(libspdlog") "message(")
+ (("ExternalProject_Add\\(libdivsufsort") "message(")
+ (("ExternalProject_Add\\(libstadenio") "message(")
+ (("ExternalProject_Add_Step\\(") "message("))
+
+ ;; Ensure that all headers can be found
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (getenv "CPLUS_INCLUDE_PATH")
+ ":"
+ (assoc-ref inputs "bwa")
+ "/include/bwa"
+ ":"
+ (assoc-ref inputs "eigen")
+ "/include/eigen3"))
+ (setenv "CPATH"
+ (string-append (assoc-ref inputs "bwa")
+ "/include/bwa"
+ ":"
+ (assoc-ref inputs "eigen")
+ "/include/eigen3"))
+ #t))
+ ;; CMAKE_INSTALL_PREFIX does not exist when the tests are
+ ;; run. It only exists after the install phase.
+ (add-after 'unpack 'fix-tests
+ (lambda _
+ (substitute* "src/CMakeLists.txt"
+ (("DTOPLEVEL_DIR=\\$\\{CMAKE_INSTALL_PREFIX")
+ "DTOPLEVEL_DIR=${GAT_SOURCE_DIR"))
+ #t)))))
+ (inputs
+ `(("boost" ,boost)
+ ("bwa" ,bwa-for-salmon)
+ ("bzip2" ,bzip2)
+ ("cereal" ,cereal)
+ ("eigen" ,eigen)
+ ("rapmap" ,(origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/COMBINE-lab/RapMap.git")
+ (commit (string-append "salmon-v" version))))
+ (file-name (string-append "rapmap-salmon-v" version "-checkout"))
+ (sha256
+ (base32
+ "1yc12yqsz6f0r8sg1qnk57xg34aqwc9jbqq6gd5ys28xw3plj98p"))))
+ ("jemalloc" ,jemalloc)
+ ("jellyfish" ,jellyfish)
+ ("libgff" ,libgff)
+ ("tbb" ,tbb)
+ ("libdivsufsort" ,libdivsufsort)
+ ("libstadenio-for-salmon" ,libstadenio-for-salmon)
+ ("spdlog-for-salmon" ,spdlog-for-salmon)
+ ("xz" ,xz)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/COMBINE-lab/salmon")
+ (synopsis "Quantification from RNA-seq reads using lightweight alignments")
+ (description "Salmon is a program to produce highly-accurate,
+transcript-level quantification estimates from RNA-seq data. Salmon achieves
+its accuracy and speed via a number of different innovations, including the
+use of lightweight alignments (accurate but fast-to-compute proxies for
+traditional read alignments) and massively-parallel stochastic collapsed
+variational inference.")
+ (license license:gpl3+)))