From c3b2ab9d3bcc0bd8562365b6720c7b135e877f55 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 17 Jan 2018 22:41:05 +0100 Subject: gnu: Add libgff. * gnu/packages/bioinformatics.scm (libgff): New variable. --- gnu/packages/bioinformatics.scm | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f0bfa9300b..f5e32ffa4d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017 Ricardo Wurmus +;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus ;;; Copyright © 2015, 2016, 2017 Ben Woodcroft ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2015 Andreas Enge @@ -11109,3 +11109,26 @@ 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")))) -- cgit 1.4.1 From 1fe0bde34dd4c0804bbbf93029059d5f92aeb354 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 17 Jan 2018 22:42:04 +0100 Subject: gnu: Add libdivsufsort. * gnu/packages/bioinformatics.scm (libdivsufsort): New variable. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f5e32ffa4d..c820f87c0b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11132,3 +11132,31 @@ 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))) -- cgit 1.4.1 From 8d77a085a7e3d15ada36041507c8c9d076a2034a Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 17 Jan 2018 22:46:04 +0100 Subject: gnu: Add sailfish. * gnu/packages/bioinformatics.scm (sailfish): New variable. --- gnu/packages/bioinformatics.scm | 147 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 147 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') 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+))) -- cgit 1.4.1 From 7762646d95cf9cad6be7e11ad465517b5819b2d2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 17 Jan 2018 23:06:52 +0100 Subject: gnu: Add salmon. * gnu/packages/bioinformatics.scm (libstadenio-for-salmon, spdlog-for-salmon, bwa-for-salmon, salmon): New variables. --- gnu/packages/bioinformatics.scm | 263 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 263 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') 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+))) -- cgit 1.4.1 From 3df57b3a9767f5b913ca69cd65e55d2aed57facb Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 22 Jan 2018 09:39:39 +0200 Subject: gnu: khmer: Add aarch64-linux to supported systems. * gnu/packages/bioinformatics.scm (khmer)[supported-systems]: Add aarch64-linux to the supported systems. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb35537a06..31d5213f95 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Roel Janssen -;;; Copyright © 2016, 2017 Efraim Flashner +;;; Copyright © 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 Marius Bakke ;;; Copyright © 2016 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice @@ -3434,7 +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 -- cgit 1.4.1 From 625cdc3fdeb16c422db8967e7bf7f4bcb424821e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 22 Jan 2018 15:47:26 +0100 Subject: gnu: star: Make reproducible. * gnu/packages/bioinformatics.scm (star)[arguments]: Add build phase "make-reproducible". --- gnu/packages/bioinformatics.scm | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31d5213f95..c96d462445 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5563,6 +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" -- cgit 1.4.1 From cd70f9bdb0f46acf3fecb5254b7df46dd258fe5b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Thu, 25 Jan 2018 21:03:31 +0100 Subject: gnu: deeptools: Update URI. * gnu/packages/bioinformatics.scm (deeptools)[source, home-page]: Update URI. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c96d462445..4d05aeb4c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2039,7 +2039,7 @@ with Python.") (version "2.5.1") (source (origin (method url-fetch) - (uri (string-append "https://github.com/fidelram/deepTools/" + (uri (string-append "https://github.com/deeptools/deepTools/" "archive/" version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 @@ -2058,7 +2058,7 @@ with Python.") `(("python-mock" ,python-mock) ;for tests ("python-nose" ,python-nose) ;for tests ("python-pytz" ,python-pytz))) ;for tests - (home-page "https://github.com/fidelram/deepTools") + (home-page "https://github.com/deeptools/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") (description "DeepTools addresses the challenge of handling the large amounts of data -- cgit 1.4.1 From a81f7eb858bf7e320d4dccde183d303247b6d47a Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 26 Jan 2018 12:47:02 +1000 Subject: gnu: diamond: Update to 0.9.15. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.15. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4d05aeb4c2..01f35dbb33 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2074,7 +2074,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.14") + (version "0.9.15") (source (origin (method url-fetch) (uri (string-append @@ -2083,7 +2083,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "07li3chjdna0wjyh680j3bhwiqh1fbfq9dy9jxxs82mc0rw0m1yy")))) + "0c9v0lddz8df5pnra464832cgn1igzpawgsknly7s1mq0qk9aiqj")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit 1.4.1 From ae8522d2659f6a37a2f9c9f85849d38eadec6e0c Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 27 Jan 2018 10:21:06 +1000 Subject: gnu: diamond: Update to 0.9.16. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.16. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 01f35dbb33..a240434e0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2074,7 +2074,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.15") + (version "0.9.16") (source (origin (method url-fetch) (uri (string-append @@ -2083,7 +2083,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0c9v0lddz8df5pnra464832cgn1igzpawgsknly7s1mq0qk9aiqj")))) + "1sydm3jldl4pypy74g82dj9j8vx3j3ikf3i9srxqjp7r64039hiy")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit 1.4.1 From 7502badb81311df8ded0202c99b7cada31511678 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 2 Feb 2018 22:12:18 +1000 Subject: gnu: diamond: Update to 0.9.17. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.17. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a240434e0d..b8c6e6ad79 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus -;;; Copyright © 2015, 2016, 2017 Ben Woodcroft +;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft ;;; Copyright © 2015, 2016 Pjotr Prins ;;; Copyright © 2015 Andreas Enge ;;; Copyright © 2016 Roel Janssen @@ -2074,7 +2074,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.16") + (version "0.9.17") (source (origin (method url-fetch) (uri (string-append @@ -2083,7 +2083,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1sydm3jldl4pypy74g82dj9j8vx3j3ikf3i9srxqjp7r64039hiy")))) + "1p3fd1ad7hg2w09w3sjk4pxqx0p0gaqys8ipg3f4adg77mn9m9yd")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit 1.4.1 From 9e94d063abbf3a686b2c5e8daf2303f2cae909a0 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Wed, 7 Feb 2018 13:06:05 +0100 Subject: gnu: multiqc: Update to 1.4. * gnu/packages/bioinformatics.scm (multiqc): Update to 1.4. [propagated-inputs]: Remove PYTHON-ENUM34. --- gnu/packages/bioinformatics.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index cf9c087ed9..b9b0dad9d7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8816,18 +8816,17 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.3") + (version "1.4") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0fx1sx53znbgzfhbbiyd8j6cg5llpcsl5q5c45jy2c81d12piqfd")))) + "0ihx4rzmsfphv4byn05qv6f1y95g2dxs6viwziipl4wjk96acgm8")))) (build-system python-build-system) (propagated-inputs - `(("python-enum34" ,python-enum34) - ("python-jinja2" ,python-jinja2) + `(("python-jinja2" ,python-jinja2) ("python-simplejson" ,python-simplejson) ("python-pyyaml" ,python-pyyaml) ("python-click" ,python-click) -- cgit 1.4.1 From aba3e482b9cc239b685f81fd718a3dc49545f1f8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Feb 2018 13:30:07 +0100 Subject: gnu: Add r-hdf5array. * gnu/packages/bioinformatics.scm (r-hdf5array): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b8c6e6ad79..9c8ff7be0c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10402,6 +10402,32 @@ problems in genomics, brain imaging, astrophysics, and data mining.") ;; Any version of the LGPL. (license license:lgpl3+))) +(define-public r-hdf5array + (package + (name "r-hdf5array") + (version "1.6.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "HDF5Array" version)) + (sha256 + (base32 + "0kcdza41saqv6vlpvqd841awbiwkg84lh0plx6c7fmfgbqv7a0jh")))) + (properties `((upstream-name . "HDF5Array"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-delayedarray" ,r-delayedarray) + ("r-iranges" ,r-iranges) + ("r-rhdf5" ,r-rhdf5) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/HDF5Array") + (synopsis "HDF5 back end for DelayedArray objects") + (description "This package provides an array-like container for convenient +access and manipulation of HDF5 datasets. It supports delayed operations and +block processing.") + (license license:artistic2.0))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 748e9f163a06b6812dfdccb2ccefcebb5cd60dcb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Feb 2018 15:18:49 +0100 Subject: gnu: Add r-rhdf5lib. * gnu/packages/bioinformatics.scm (r-rhdf5lib): New variable. --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9c8ff7be0c..0dbb1f1764 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10428,6 +10428,62 @@ access and manipulation of HDF5 datasets. It supports delayed operations and block processing.") (license license:artistic2.0))) +(define-public r-rhdf5lib + (package + (name "r-rhdf5lib") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Rhdf5lib" version)) + (sha256 + (base32 + "0kkc4rprjbqn2wvbx4d49kk9l91vihccxbl4843qr1wqk6v33r1w")))) + (properties `((upstream-name . "Rhdf5lib"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'do-not-use-bundled-hdf5 + (lambda* (#:key inputs #:allow-other-keys) + (for-each delete-file '("configure" "configure.ac")) + ;; Do not make other packages link with the proprietary libsz. + (substitute* "R/zzz.R" + (("'%s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a'") + "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a'") + (("'%s/libhdf5.a %s/libsz.a'") + "'%s/libhdf5.a %s/libhdf5.a'")) + (with-directory-excursion "src" + (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) + (rename-file (string-append "hdf5-" ,(package-version hdf5)) + "hdf5") + (rename-file "Makevars.in" "Makevars") + (substitute* "Makevars" + (("HDF5_CXX_LIB=.*") + (string-append "HDF5_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n")) + (("HDF5_LIB=.*") + (string-append "HDF5_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5.a\n")) + (("HDF5_CXX_INCLUDE=.*") "HDF5_CXX_INCLUDE=./hdf5/c++/src\n") + (("HDF5_INCLUDE=.*") "HDF5_INCLUDE=./hdf5/src\n") + ;; szip is non-free software + (("cp \\$\\{SZIP_LIB\\}.*") "") + (("PKG_LIBS = \\$\\{HDF5_LIB\\} \\$\\{SZIP_LIB\\}") + "PKG_LIBS = ${HDF5_LIB}\n"))) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("hdf5" ,hdf5))) + (native-inputs + `(("hdf5-source" ,(package-source hdf5)))) + (home-page "https://bioconductor.org/packages/Rhdf5lib") + (synopsis "HDF5 library as an R package") + (description "This package provides C and C++ HDF5 libraries for use in R +packages.") + (license license:artistic2.0))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 9ec08988249312d4f09d0e2e9da0164764783b12 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Feb 2018 15:19:00 +0100 Subject: gnu: Add r-beachmat. * gnu/packages/bioinformatics.scm (r-beachmat): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0dbb1f1764..a5a4abb1dd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10484,6 +10484,33 @@ block processing.") packages.") (license license:artistic2.0))) +(define-public r-beachmat + (package + (name "r-beachmat") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beachmat" version)) + (sha256 + (base32 + "0b6dzja5fbx4dawb7ixj67mlhw4fy62pfp20mfp918fy96zmdwqz")))) + (build-system r-build-system) + (inputs + `(("hdf5" ,hdf5))) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-hdf5array" ,r-hdf5array) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib))) + (home-page "https://bioconductor.org/packages/beachmat") + (synopsis "Compiling Bioconductor to handle each matrix type") + (description "This package provides a consistent C++ class interface for a +variety of commonly used matrix types, including sparse and HDF5-backed +matrices.") + (license license:gpl3))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 6fb1dc17a3898eb04178235d86aa0da480523d34 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Feb 2018 15:19:11 +0100 Subject: gnu: Add r-singlecellexperiment. * gnu/packages/bioinformatics.scm (r-singlecellexperiment): New variable. --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a5a4abb1dd..912769efb7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10511,6 +10511,33 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +(define-public r-singlecellexperiment + (package + (name "r-singlecellexperiment") + (version "1.0.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "SingleCellExperiment" version)) + (sha256 + (base32 + "1r276i97w64a5vdlg6952gkj7bls909p42zl8fn8yz87cdwyaars")))) + (properties + `((upstream-name . "SingleCellExperiment"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (home-page "https://bioconductor.org/packages/SingleCellExperiment") + (synopsis "S4 classes for single cell data") + (description "This package defines an S4 class for storing data from +single-cell experiments. This includes specialized methods to store and +retrieve spike-in information, dimensionality reduction coordinates and size +factors for each cell, along with the usual metadata for genes and +libraries.") + (license license:gpl3))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 658ab21d2e16bda0a8c3cfc8f4cc4715628b6247 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Feb 2018 15:19:25 +0100 Subject: gnu: Add r-scater. * gnu/packages/bioinformatics.scm (r-scater): New variable. Co-authored-by: Raoul Jean Pierre Bonnal --- gnu/packages/bioinformatics.scm | 46 ++++++++++++++++++++++++++++++++++++++++- 1 file changed, 45 insertions(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 912769efb7..16bb1c0f8d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2016 Roel Janssen ;;; Copyright © 2016, 2017, 2018 Efraim Flashner ;;; Copyright © 2016 Marius Bakke -;;; Copyright © 2016 Raoul Bonnal +;;; Copyright © 2016, 2018 Raoul Bonnal ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice ;;; Copyright © 2017 Arun Isaac ;;; @@ -10538,6 +10538,50 @@ factors for each cell, along with the usual metadata for genes and libraries.") (license license:gpl3))) +(define-public r-scater + (package + (name "r-scater") + (version "1.6.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scater" version)) + (sha256 + (base32 + "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biomart" ,r-biomart) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-edger" ,r-edger) + ("r-ggbeeswarm" ,r-ggbeeswarm) + ("r-ggplot2" ,r-ggplot2) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-plyr" ,r-plyr) + ("r-rcpp" ,r-rcpp) + ("r-reshape2" ,r-reshape2) + ("r-rhdf5" ,r-rhdf5) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-rjson" ,r-rjson) + ("r-s4vectors" ,r-s4vectors) + ("r-shiny" ,r-shiny) + ("r-shinydashboard" ,r-shinydashboard) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-tximport" ,r-tximport) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/davismcc/scater") + (synopsis "Single-cell analysis toolkit for gene expression data in R") + (description "This package provides a collection of tools for doing +various analyses of single-cell RNA-seq gene expression data, with a focus on +quality control.") + (license license:gpl2+))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 7f1d9bef503e546eb3572e7930793dcbe0d2407e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 12 Feb 2018 15:29:15 +0100 Subject: gnu: Add r-scran. * gnu/packages/bioinformatics.scm (r-scran): New variable. --- gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 16bb1c0f8d..ea92e93703 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10582,6 +10582,48 @@ various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.") (license license:gpl2+))) +(define-public r-scran + (package + (name "r-scran") + (version "1.6.7") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scran" version)) + (sha256 + (base32 + "0zfm5i8xrnzb3894xygqd6zkbwaa2x3z74wbxw39fcjhyhxv2hmb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-dt" ,r-dt) + ("r-dynamictreecut" ,r-dynamictreecut) + ("r-edger" ,r-edger) + ("r-fnn" ,r-fnn) + ("r-ggplot2" ,r-ggplot2) + ("r-igraph" ,r-igraph) + ("r-limma" ,r-limma) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-rhdf5lib" ,r-rhdf5lib) + ("r-s4vectors" ,r-s4vectors) + ("r-scater" ,r-scater) + ("r-shiny" ,r-shiny) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-statmod" ,r-statmod) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-viridis" ,r-viridis) + ("r-zoo" ,r-zoo))) + (home-page "https://bioconductor.org/packages/scran") + (synopsis "Methods for single-cell RNA-Seq data analysis") + (description "This package implements a variety of low-level analyses of +single-cell RNA-seq data. Methods are provided for normalization of +cell-specific biases, assignment of cell cycle phase, and detection of highly +variable and significantly correlated genes.") + (license license:gpl3))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 2e9da3390cd397ab3861d2fe9662f89c6b9d3913 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:54:09 +0100 Subject: gnu: r-vegan: Update to 2.4-6. * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ea92e93703..613f238ffd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5849,14 +5849,14 @@ information as possible.") (define-public r-vegan (package (name "r-vegan") - (version "2.4-5") + (version "2.4-6") (source (origin (method url-fetch) (uri (cran-uri "vegan" version)) (sha256 (base32 - "0cyyvn3xsjn24w590jn6z4xajafv7yzvj6c51vqi9q6m8v5831ya")))) + "175mqr42mmxy98gpf3rky8alnkw3w1k90ggdw3cispl36841p76w")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) -- cgit 1.4.1 From 66ae706c2460cc0e58a7b41b7689dc261c49d964 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:54:25 +0100 Subject: gnu: r-bookdown: Update to 0.6. * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.6. [propagated-inputs]: Add r-xfun and ghc-pandoc. --- gnu/packages/bioinformatics.scm | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 613f238ffd..7689600a4d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6673,19 +6673,21 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.5") + (version "0.6") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "0zm63kr4f4kja4qpwkzl119zzyciqj7ihajfqgfjpgb4dzaiycxp")))) + "1pxxln42kvzl38fjprg6hcnyh1kij75fpj70vwp5hp5il813aszc")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) ("r-knitr" ,r-knitr) ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) + ("r-yaml" ,r-yaml) + ("r-xfun" ,r-xfun) + ("ghc-pandoc" ,ghc-pandoc))) (home-page "https://github.com/rstudio/bookdown") (synopsis "Authoring books and technical documents with R markdown") (description "This package provides output formats and utilities for -- cgit 1.4.1 From d22abe1e5dd7c9560ea231bb2b4359dc29c99a25 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:54:51 +0100 Subject: gnu: r-edger: Update to 3.20.8. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.8. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7689600a4d..f11cbbb736 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6967,13 +6967,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.20.2") + (version "3.20.8") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0j5s3i33qmld9l7gs1rzpv601zxyqz711x8mq35hml088c8s99w9")))) + "0g7bj6w61blw3m22hw9rc01n554k9qkjizh7njr3j4shmhads58d")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5fb1fee67b41f8f57f7abd72f7e536c8d496b529 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:55:12 +0100 Subject: gnu: r-variantannotation: Update to 1.24.5. * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.24.5. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f11cbbb736..c286a24fa8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6995,13 +6995,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.24.2") + (version "1.24.5") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "19wgb2kcqy97pm3xgqc781id9fbmzp1hdwzkkhdzpvyf29w4n29j")))) + "07ywn3c4w83l3sr76d0z3b1nv9icgdh3phsjlc6cfx7i6nfmvxw2")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs -- cgit 1.4.1 From 0674657908b150cbaafd9c0952983dad23bec897 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:55:27 +0100 Subject: gnu: r-limma: Update to 3.34.8. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.34.8. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c286a24fa8..91ae28d552 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7033,13 +7033,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.34.4") + (version "3.34.8") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1vcxf9jg8xngxg5kb9bp8rw5sghpnkpj320iq309m2fp41ahsk3f")))) + "0bmxsgz2yll83sd3wbxsrsfd35468igb0d8lldym0d0lqfz906bw")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit 1.4.1 From 024f19c68b253c4a1755847285a8587605b1c0a4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:58:15 +0100 Subject: gnu: r-genomicranges: Update to 1.30.1. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 91ae28d552..534f5e79e6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7088,13 +7088,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "10ra2sjn17h6gilm9iz0cygp9ijpgbirljlc4drwrnivnw9cmi2a")))) + "1wnvvhj8yjsx242y6kfr5vs8kzisa96rxl1rgnnychrrvnvnh3i1")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit 1.4.1 From 373430672d5425cddb079c77bcbdad904b2db0de Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:58:32 +0100 Subject: gnu: r-biomart: Update to 2.34.2. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 534f5e79e6..e9eed753a9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7166,13 +7166,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.34.1") + (version "2.34.2") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "0jzv8b86vpvavwnzi5xf7y18xmn72zkabkn2kclg1mgl847cq13k")))) + "1zlgs2zg0lmnk572p55n7m34nkxka8w10x8f2ndssjkffl2csy79")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit 1.4.1 From c37b361e44eb3ac150c6bc9e790ef6fae28ec1b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:58:47 +0100 Subject: gnu: r-summarizedexperiment: Update to 1.8.1. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.8.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e9eed753a9..7563281904 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7324,13 +7324,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1011r8l0k8420j31bmh4xdcp6ka5bzf4bqhip84v5b6alpkcbvmf")))) + "19vlwnby83fqjrilsxvnvgz0gvby7mrxvlmx18nb3p1w591ddfjh")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit 1.4.1 From 99b3236e65b3a05ed59617bec7a24cafdf5596d6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:59:01 +0100 Subject: gnu: r-rtracklayer: Update to 1.38.3. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7563281904..22ee3f10b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7388,13 +7388,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.38.2") + (version "1.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1sjn3976f1sqvrq6jq2hgc60ffxgfr3jlklaxfrk3xad5cv2kr2d")))) + "1khzfczm35k5lq9h0jlqrq01192spzjyh8s6is89spj006flwn4k")))) (build-system r-build-system) (arguments `(#:phases -- cgit 1.4.1 From 0b18856532c8a91ce17b6615b2e8a6be3844d7a8 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:59:21 +0100 Subject: gnu: r-genomicfeatures: Update to 1.30.3. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 22ee3f10b5..f38165c20d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7433,13 +7433,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.30.0") + (version "1.30.3") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "1khjvq1ffhqavkwf8n7bilknci60lxbg52icrcf2vnb9k8rlpghs")))) + "010vn8hlwbnw12pd1d8pv6m12yp3xwx557gba5rbjq9p4qypnn3z")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit 1.4.1 From e1129446ecd02b9cc3343c19188d253536907821 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:59:36 +0100 Subject: gnu: r-genomation: Update to 1.11.3. * gnu/packages/bioinformatics.scm (r-genomation): Update to 1.11.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f38165c20d..60c4a21265 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7659,13 +7659,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.10.0") + (version "1.11.3") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "1ddd8c9w1f1i1ga9rpbwiic8rsaws1chdxx4j38bpyaiy4zhz1ca")))) + "1d2g1v6xhrf3gm86pv8ln22df5g6v6k6i4i39v4j82zn4apany6v")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) -- cgit 1.4.1 From 0b24dc95b58d06a352784a76c4e078afe0cb7ad7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 15:59:50 +0100 Subject: gnu: r-wgcna: Update to 1.62. * gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.62. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 60c4a21265..b32b1c911c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8364,14 +8364,14 @@ in SNV base substitution data.") (define-public r-wgcna (package (name "r-wgcna") - (version "1.61") + (version "1.62") (source (origin (method url-fetch) (uri (cran-uri "WGCNA" version)) (sha256 (base32 - "1vrc2k33a196hrrl7k0z534fp96vv0shmigcr65ny1q0v6lq0h6i")))) + "0c52rp09gqphz6g5x9jzkdcsyvfrknq0dkq9saslgy8q8ap974vx")))) (properties `((upstream-name . "WGCNA"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 5ef76bc28ca0de59827741ac6a53f6e55f984d8d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:00:03 +0100 Subject: gnu: r-gkmsvm: Update to 0.79.0. * gnu/packages/bioinformatics.scm (r-gkmsvm): Update to 0.79.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b32b1c911c..f8697faffb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8469,14 +8469,14 @@ factors bound at the specific regions.") (define-public r-gkmsvm (package (name "r-gkmsvm") - (version "0.71.0") + (version "0.79.0") (source (origin (method url-fetch) (uri (cran-uri "gkmSVM" version)) (sha256 (base32 - "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0")))) + "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) (properties `((upstream-name . "gkmSVM"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From b1f275362748b975e4100199cbf8b3080b671ca7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:00:18 +0100 Subject: gnu: r-methylkit: Update to 1.4.1. * gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.4.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f8697faffb..bf53f9e91c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8944,13 +8944,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0h53w2mrjrg2n0ndi12k9j6cwclgwcgpy25nz7nyj971aisw02xn")))) + "1k0nfn9318sgwm4z963bhnbp4c3zv85v3f9886vc5hgaisr0yvai")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 53f0dea9d75cfdf814a3744c11ee71e16e23ef78 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:00:32 +0100 Subject: gnu: r-msnbase: Update to 2.4.2. * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bf53f9e91c..c0cc88f789 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9314,14 +9314,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.4.0") + (version "2.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0dqfimljhrx3gac8d1k72gppx27lz8yckyb12v4604nbviw7xd3r")))) + "1ig64bf881p118dwqfr0ry41m7yhnyv165smv8fdwfv7sb6sagif")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 26e3e28cc9a55d52415d1fa7733eaae34d4ba4e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:00:56 +0100 Subject: gnu: r-seurat: Update to 2.2.0. * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.0. [propagated-inputs]: Remove r-ggjoy; add r-rcppeigen and r-ggridges. --- gnu/packages/bioinformatics.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c0cc88f789..1e2455d874 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9394,13 +9394,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.1.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1hqaq6bciikrsyw157w8fn4jw885air7xbkxrmism93rp4qx483x")) + "1yarzhbylkfk4vwp7f8710zpdglkfww2db3hmq69hjllgg80ykmw")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9437,8 +9437,8 @@ Main-Class: ModularityOptimizer\n"))) ("r-fnn" ,r-fnn) ("r-fpc" ,r-fpc) ("r-gdata" ,r-gdata) - ("r-ggjoy" ,r-ggjoy) ("r-ggplot2" ,r-ggplot2) + ("r-ggridges" ,r-ggridges) ("r-gplots" ,r-gplots) ("r-gridextra" ,r-gridextra) ("r-hmisc" ,r-hmisc) @@ -9455,6 +9455,7 @@ Main-Class: ModularityOptimizer\n"))) ("r-ranger" ,r-ranger) ("r-rcolorbrewer" ,r-rcolorbrewer) ("r-rcpp" ,r-rcpp) + ("r-rcppeigen" ,r-rcppeigen) ("r-rcppprogress" ,r-rcppprogress) ("r-reshape2" ,r-reshape2) ("r-rocr" ,r-rocr) -- cgit 1.4.1 From f5f9442703cc819e24136c42373ac34b06466533 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:01:35 +0100 Subject: gnu: r-keggrest: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-keggrest): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e2455d874..9be5370749 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9665,14 +9665,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "1i3i88lj57wvpgjf75a23msgfsjv8pr2b4j1faga276p4fsblkhj")))) + "02gwmm79djj55a90dzc80hlgwc6bafl7xd7fnx2q59pk945k3z9c")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 34d077b8bc79b4baf725b91b10ff78f47e478b68 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:01:49 +0100 Subject: gnu: r-gage: Update to 2.28.2. * gnu/packages/bioinformatics.scm (r-gage): Update to 2.28.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9be5370749..c5b60b52aa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9689,14 +9689,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.28.0") + (version "2.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "1r14p88q3y736pkqm4pdimf1izy1xy3xgivmj3cr4dv65kjny1zk")))) + "0h0mlhns9j7cpfksvdlvx9jb7szm3r1dwqb3s4s8p8hmkb9byyii")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 169942368fb8d3cf47227692ac967d981d4c2820 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:02:00 +0100 Subject: gnu: r-ensembldb: Update to 2.2.1. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c5b60b52aa..439289e4ac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9810,14 +9810,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1w0lca3ws5j770bmls91cn93lznvv2pc8s42nybdzz3vdxjvb4m1")))) + "1vk6j0r5cczxmwbfzzkgayna66rxkfa3q2jikz649qvdiybhls40")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From 97bf74076c59d4b3c97d78b5baafbe47ae592ad2 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 13 Feb 2018 16:02:13 +0100 Subject: gnu: r-gprofiler: Update to 0.6.3. * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 439289e4ac..31e739e0b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9979,14 +9979,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.1") + (version "0.6.3") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "1qix15d0wa9nspdclcawml94mng4qmr2jciv7d24py315wfsvv8p")))) + "08dsnja3g8qvqlgwhx9c9f8p8psn3qr5ddn84dhizkgglj30v2wj")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 119c09c2196a2c4aa1cd9dbeec7a38a9dae0a1d6 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Wed, 14 Feb 2018 07:43:19 +1000 Subject: gnu: vsearch: Update to 2.7.0. * gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.0. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 31e739e0b5..14a790bef0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6370,7 +6370,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.6.2") + (version "2.7.0") (source (origin (method url-fetch) @@ -6380,7 +6380,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "02khrgh8hm11cgww2f9mqc6886zqli9ss4pd4kfpqzd0d31vbzv5")) + "0523b8xq5fw60ayl0k5m1fm6yrh1932ljrsz1ys67xnki7p7f1d5")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin -- cgit 1.4.1 From 05f7296012b8a4bd6429abcaf6ff5000033a44c1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Feb 2018 14:27:43 +0100 Subject: gnu: Add r-delayedmatrixstats. * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): New variable. --- gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 41b7446915..548b045599 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10626,6 +10626,38 @@ cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.") (license license:gpl3))) +(define-public r-delayedmatrixstats + (package + (name "r-delayedmatrixstats") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedMatrixStats" version)) + (sha256 + (base32 + "1nfdan0k2z4mynxyblsil0cjclsy63b0w9r1hczfk27i8hmxx13h")))) + (properties + `((upstream-name . "DelayedMatrixStats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixstats" ,r-matrixstats) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/PeteHaitch/DelayedMatrixStats") + (synopsis "Functions that apply to rows and columns of DelayedMatrix objects") + (description + "This package provides a port of the @code{matrixStats} API for use with +@code{DelayedMatrix} objects from the @code{DelayedArray} package. It +contains high-performing functions operating on rows and columns of +@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians}, +@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions +are optimized per data type and for subsetted calculations such that both +memory usage and processing time is minimized.") + (license license:expat))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 3082de04c2b193bf2db2312c9ea28c18bb28bdf4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Feb 2018 14:27:50 +0100 Subject: gnu: Add r-dropbead. * gnu/packages/bioinformatics.scm (r-dropbead): New variable. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 548b045599..0206eb35b5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10658,6 +10658,35 @@ are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.") (license license:expat))) +(define-public r-dropbead + (let ((commit "cf0be5ae5302684bd03e78ab65b142900bbbb840") + (revision "1")) + (package + (name "r-dropbead") + (version (string-append "0-" revision "." (string-take commit 7))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rajewsky-lab/dropbead.git") + (commit commit))) + (sha256 + (base32 + "1b2lphsc236s1rdzlijxg8yl1jnqpwcvj4x938r89rqpj93jb780")))) + (build-system r-build-system) + (propagated-inputs + `(("r-ggplot2" ,r-ggplot2) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-gridextra" ,r-gridextra) + ("r-gplots" ,r-gplots) + ("r-plyr" ,r-plyr))) + (home-page "https://github.com/rajewsky-lab/dropbead") + (synopsis "Basic exploration and analysis of Drop-seq data") + (description "This package offers a quick and straight-forward way to +explore and perform basic analysis of single cell sequencing data coming from +droplet sequencing. It has been particularly tailored for Drop-seq.") + (license license:gpl3)))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package -- cgit 1.4.1 From 152d30c34690c00cc96053a9ae6196b26e93ba84 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 14 Feb 2018 14:28:00 +0100 Subject: gnu: Add python-loompy. * gnu/packages/bioinformatics.scm (python-loompy): New variable. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0206eb35b5..f790737f5e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11857,3 +11857,31 @@ use of lightweight alignments (accurate but fast-to-compute proxies for traditional read alignments) and massively-parallel stochastic collapsed variational inference.") (license license:gpl3+))) + +(define-public python-loompy + (package + (name "python-loompy") + (version "2.0.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "loompy" version)) + (sha256 + (base32 + "1drgv8j1hxqzzpnfg272x9djb6j8qr798w1pc2x8ikmfgyd9gh51")))) + (build-system python-build-system) + ;; There are no tests + (arguments '(#:tests? #f)) + (propagated-inputs + `(("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy) + ("python-typing" ,python-typing))) + (home-page "https://github.com/linnarsson-lab/loompy") + (synopsis "Work with .loom files for single-cell RNA-seq data") + (description "The loom file format is an efficient format for very large +omics datasets, consisting of a main matrix, optional additional layers, a +variable number of row and column annotations. Loom also supports sparse +graphs. This library makes it easy to work with @file{.loom} files for +single-cell RNA-seq data.") + (license license:bsd-3))) -- cgit 1.4.1 From 5ebc8e7f41bfc292dedb9de3bf13b54bc0d0d2dd Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Fri, 16 Feb 2018 08:13:24 +1000 Subject: gnu: diamond: Update to 0.9.18. * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.18. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 14a790bef0..00490dbcbb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2074,7 +2074,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.17") + (version "0.9.18") (source (origin (method url-fetch) (uri (string-append @@ -2083,7 +2083,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1p3fd1ad7hg2w09w3sjk4pxqx0p0gaqys8ipg3f4adg77mn9m9yd")))) + "1vi2nddmy7knrv8gsprwqp6a40k63n3f2dfvx22ipjhrg9xir96f")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target -- cgit 1.4.1 From 369eee8763ca34b427860a86c8fe2db0963b52ae Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Sat, 17 Feb 2018 12:44:29 +1000 Subject: gnu: vsearch: Update to 2.7.1. * gnu/packages/bioinformatics.scm (vsearch): Update to 2.7.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 00490dbcbb..86c303f2b1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6370,7 +6370,7 @@ SELECT or UPDATE queries to an end-point.") (define-public vsearch (package (name "vsearch") - (version "2.7.0") + (version "2.7.1") (source (origin (method url-fetch) @@ -6380,7 +6380,7 @@ SELECT or UPDATE queries to an end-point.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0523b8xq5fw60ayl0k5m1fm6yrh1932ljrsz1ys67xnki7p7f1d5")) + "0jlzfgh79fzmb4g7sngzdjjsjyc37icvs1k7vmc2ksxglj6x5i7f")) (patches (search-patches "vsearch-unbundle-cityhash.patch")) (snippet '(begin -- cgit 1.4.1 From 9800f7d9e81f259c9041fffb5dc14930bff3379d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:49:25 +0100 Subject: gnu: r-bookdown: Update to 0.7. * gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.7. [propagated-inputs]: Add r-tinytex. --- gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++-------------------- 1 file changed, 21 insertions(+), 20 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2c8dc8f399..354a809c44 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6672,27 +6672,28 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package - (name "r-bookdown") - (version "0.6") - (source (origin - (method url-fetch) - (uri (cran-uri "bookdown" version)) - (sha256 - (base32 - "1pxxln42kvzl38fjprg6hcnyh1kij75fpj70vwp5hp5il813aszc")))) - (build-system r-build-system) - (propagated-inputs - `(("r-htmltools" ,r-htmltools) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml) - ("r-xfun" ,r-xfun) - ("ghc-pandoc" ,ghc-pandoc))) - (home-page "https://github.com/rstudio/bookdown") - (synopsis "Authoring books and technical documents with R markdown") - (description "This package provides output formats and utilities for + (name "r-bookdown") + (version "0.7") + (source (origin + (method url-fetch) + (uri (cran-uri "bookdown" version)) + (sha256 + (base32 + "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q")))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-tinytex" ,r-tinytex) + ("r-yaml" ,r-yaml) + ("r-xfun" ,r-xfun) + ("ghc-pandoc" ,ghc-pandoc))) + (home-page "https://github.com/rstudio/bookdown") + (synopsis "Authoring books and technical documents with R markdown") + (description "This package provides output formats and utilities for authoring books and technical documents with R Markdown.") - (license license:gpl3))) + (license license:gpl3))) (define-public r-biocstyle (package -- cgit 1.4.1 From e8484711c6682cbda98303a890afcf61778b3eac Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:50:46 +0100 Subject: gnu: r-getopt: Update to 1.20.2. * gnu/packages/bioinformatics.scm (r-getopt): Update to 1.20.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 354a809c44..a76f21edd5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6769,14 +6769,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-getopt (package (name "r-getopt") - (version "1.20.1") + (version "1.20.2") (source (origin (method url-fetch) (uri (cran-uri "getopt" version)) (sha256 (base32 - "0m463mcvixh54i3ng42n0vxmdlf97dgbfs2sf9wnjm782ddw68hm")))) + "13p35lbpy7i578752fa71sbfvcsqw5qfa9p6kf8b5m3c5p9i4v1x")))) (build-system r-build-system) (home-page "https://github.com/trevorld/getopt") (synopsis "Command-line option processor for R") -- cgit 1.4.1 From 824c2004758d0ec2340894eb2698e83316107813 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:50:57 +0100 Subject: gnu: r-genomicranges: Update to 1.30.2. * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.30.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a76f21edd5..9e51593848 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7089,13 +7089,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.30.1") + (version "1.30.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1wnvvhj8yjsx242y6kfr5vs8kzisa96rxl1rgnnychrrvnvnh3i1")))) + "0c3r155603vb4zjs3adqa72770bh8karc11y8gl62l1m24jrkbnj")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) -- cgit 1.4.1 From 3118b28644a006f53c583dc3c6b67a5703b65685 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:51:11 +0100 Subject: gnu: r-qtl: Update to 1.42-7. * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.42-7. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9e51593848..4553e8b443 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8111,7 +8111,7 @@ throughput genetic sequencing data sets using regression methods.") (define-public r-qtl (package (name "r-qtl") - (version "1.41-6") + (version "1.42-7") (source (origin (method url-fetch) @@ -8119,7 +8119,7 @@ throughput genetic sequencing data sets using regression methods.") version ".tar.gz")) (sha256 (base32 - "067az4v432zxp6lxck8d7vlh9w4r13r0mvw5zsglyaqwsh3d9sad")))) + "0hxij8v4my5x4pf5fn5327g7m3n7vjkbzrl580vcmp81n3n3nmrx")))) (build-system r-build-system) (home-page "http://rqtl.org/") (synopsis "R package for analyzing QTL experiments in genetics") -- cgit 1.4.1 From ebec98ae1d42b9a12185f0a9b261fe27441c7c3d Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:51:25 +0100 Subject: gnu: r-seurat: Update to 2.2.1. * gnu/packages/bioinformatics.scm (r-seurat): Update to 2.2.1. [propagated-inputs]: Remove r-nmf; add r-metap. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4553e8b443..e4780cfd92 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9394,13 +9394,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "2.2.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "1yarzhbylkfk4vwp7f8710zpdglkfww2db3hmq69hjllgg80ykmw")) + "1sr82nf38hq07avrfn8vlrzjq7dfm4pcr8l1nh6mnglcql2bk9z2")) ;; Delete pre-built jar. (snippet '(begin (delete-file "inst/java/ModularityOptimizer.jar") @@ -9448,8 +9448,8 @@ Main-Class: ModularityOptimizer\n"))) ("r-lars" ,r-lars) ("r-mass" ,r-mass) ("r-matrix" ,r-matrix) + ("r-metap" ,r-metap) ("r-mixtools" ,r-mixtools) - ("r-nmf" ,r-nmf) ("r-pbapply" ,r-pbapply) ("r-plotly" ,r-plotly) ("r-ranger" ,r-ranger) -- cgit 1.4.1 From 8877ab432e81eeb204957525c8f87df582fb8a49 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:51:49 +0100 Subject: gnu: r-ensembldb: Update to 2.2.2. * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.2.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e4780cfd92..70a0822a7c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9810,14 +9810,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.2.1") + (version "2.2.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "1vk6j0r5cczxmwbfzzkgayna66rxkfa3q2jikz649qvdiybhls40")))) + "1yngndkf3588z91z0a2fvkg423p26ajm6xv1p27x0l9mzhhaqq3k")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) -- cgit 1.4.1 From ca7855fcd2cc162556054d709e7a435ef7455288 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:52:00 +0100 Subject: gnu: r-gprofiler: Update to 0.6.4. * gnu/packages/bioinformatics.scm (r-gprofiler): Update to 0.6.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 70a0822a7c..37de865142 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9979,14 +9979,14 @@ interval to data view, mismatch pileup, and several splicing summaries.") (define-public r-gprofiler (package (name "r-gprofiler") - (version "0.6.3") + (version "0.6.4") (source (origin (method url-fetch) (uri (cran-uri "gProfileR" version)) (sha256 (base32 - "08dsnja3g8qvqlgwhx9c9f8p8psn3qr5ddn84dhizkgglj30v2wj")))) + "1cka02zbz1rbppm782qpxk1xn9qxbrv2gp5rgf970j906hxm2y0b")))) (properties `((upstream-name . "gProfileR"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From d578278e35a40c9b0c977cda6f12579f8cb761f6 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:52:12 +0100 Subject: gnu: r-gviz: Update to 1.22.3. * gnu/packages/bioinformatics.scm (r-gviz): Update to 1.22.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 37de865142..fb1b23d6c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10218,14 +10218,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.22.2") + (version "1.22.3") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "173n99mc95sij2vb8n3xd016x7mxhjs961q3l29xkg1lrnnm2sva")))) + "1grjzrjpzkw572pbvpsvdnfkfgwybl0cnjd7nnk2xdr26wnbsi9a")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs -- cgit 1.4.1 From 59b2864d6c46405e04bed0ec8ae765096a30608e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:52:25 +0100 Subject: gnu: r-scater: Update to 1.6.3. * gnu/packages/bioinformatics.scm (r-scater): Update to 1.6.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fb1b23d6c2..93a4f128e1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10544,13 +10544,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.6.2") + (version "1.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "0fp68n0xnbf90wrprqawsbilg9x7v2scp0dxb3936g20025csrdd")))) + "0q3s96gf8saa1dq2fvmpl0jyj7bx3wrdfck3hanb8pxkcir2p7dn")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) -- cgit 1.4.1 From 79c6af13d08f7d4563c343a2c3e9ebbc82d7695b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Sun, 18 Feb 2018 21:52:38 +0100 Subject: gnu: r-delayedmatrixstats: Update to 1.0.3. * gnu/packages/bioinformatics.scm (r-delayedmatrixstats): Update to 1.0.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 93a4f128e1..820bd84d66 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10630,14 +10630,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.0.2") + (version "1.0.3") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1nfdan0k2z4mynxyblsil0cjclsy63b0w9r1hczfk27i8hmxx13h")))) + "1cxjbjdq9hg9cm95rci0al7a4pk2h73ym276ahw9q4977zbg6381")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) -- cgit 1.4.1