diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 147 |
1 files changed, 147 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c820f87c0b..c8fa1c2999 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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+))) |