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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 263 |
1 files changed, 263 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c8fa1c2999..eb35537a06 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+))) |