diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 472 |
1 files changed, 469 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d3b137513c..12cfed68ad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,10 +1,10 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> -;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> @@ -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) @@ -3433,7 +3434,7 @@ sometimes better. Khmer can also identify and fix problems with shotgun data.") ;; When building on i686, armhf and mips64el, we get the following error: ;; error: ['khmer', 'khmer.tests', 'oxli'] require 64-bit operating system - (supported-systems '("x86_64-linux")) + (supported-systems '("x86_64-linux" "aarch64-linux")) (license license:bsd-3))) (define-public kaiju @@ -5562,6 +5563,11 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.") (modify-phases %standard-phases (add-after 'unpack 'enter-source-dir (lambda _ (chdir "source") #t)) + (add-after 'enter-source-dir 'make-reproducible + (lambda _ + (substitute* "Makefile" + (("(COMPILATION_TIME_PLACE=\")(.*)(\")" _ pre mid post) + (string-append pre "Built with Guix" post))))) (add-after 'enter-source-dir 'do-not-use-bundled-htslib (lambda _ (substitute* "Makefile" @@ -11106,3 +11112,463 @@ for alignment. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools.") (license license:bsd-2))) + +(define-public libgff + (package + (name "libgff") + (version "1.0") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/Kingsford-Group/" + "libgff/archive/v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0vc4nxyhlm6g9vvmx5l4lfs5pnvixsv1hiiy4kddf2y3p6jna8ls")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; no tests included + (home-page "https://github.com/Kingsford-Group/libgff") + (synopsis "Parser library for reading/writing GFF files") + (description "This is a simple \"libraryfication\" of the GFF/GTF parsing +code that is used in the Cufflinks codebase. The goal of this library is to +provide this functionality without the necessity of drawing in a heavy-weight +dependency like SeqAn.") + (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt")))) + +(define-public libdivsufsort + (package + (name "libdivsufsort") + (version "2.0.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/y-256/libdivsufsort.git") + (commit version))) + (sha256 + (base32 + "0fgdz9fzihlvjjrxy01md1bv9vh12rkgkwbm90b1hj5xpbaqp7z2")))) + (build-system cmake-build-system) + (arguments + '(#:tests? #f ; there are no tests + #:configure-flags + ;; Needed for rapmap and sailfish. + '("-DBUILD_DIVSUFSORT64=ON"))) + (home-page "https://github.com/y-256/libdivsufsort") + (synopsis "Lightweight suffix-sorting library") + (description "libdivsufsort is a software library that implements a +lightweight suffix array construction algorithm. This library provides a +simple and an efficient C API to construct a suffix array and a +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+))) + +(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+))) |