diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 252 |
1 files changed, 180 insertions, 72 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3387a2571a..90092ddf70 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -108,6 +108,9 @@ (base32 "0959fiiy11rzfzrzaknmgrx64bhszj02l0ycz79k5a6bmpfzanlk")))) (build-system r-build-system) + (propagated-inputs + `(("r-lattice" ,r-lattice) + ("r-nlme" ,r-nlme))) (home-page "http://ape-package.ird.fr/") (synopsis "Analyses of phylogenetics and evolution") (description @@ -475,7 +478,7 @@ BED, GFF/GTF, VCF.") (inputs `(("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) - ("r" ,r) + ("r-minimal" ,r-minimal) ("r-foreach" ,r-foreach) ("r-xnomial" ,r-xnomial) ("r-domc" ,r-domc) @@ -1725,7 +1728,7 @@ gene predictor designed to work with assembled, aligned RNA-seq transcripts.") ("python2-scipy" ,python2-scipy) ("python2-matplotlib" ,python2-matplotlib))) (propagated-inputs - `(("r" ,r) + `(("r-minimal" ,r-minimal) ("libsvm" ,libsvm) ("randomjungle" ,randomjungle))) (native-inputs @@ -4001,7 +4004,7 @@ partial genes, and identifies translation initiation sites.") ("grep" ,grep) ("sed" ,sed) ("gawk" ,gawk) - ("r" ,r) + ("r-minimal" ,r-minimal) ("r-ggplot2" ,r-ggplot2) ("coreutils" ,coreutils))) (home-page "http://sanger-pathogens.github.io/Roary") @@ -4116,7 +4119,7 @@ phylogenies.") (inputs `(("boost" ,boost) ("ncurses" ,ncurses) - ("r" ,r) + ("r-minimal" ,r-minimal) ("perl" ,perl) ("samtools" ,samtools-0.1) ("zlib" ,zlib))) @@ -4383,7 +4386,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (define-public ngs-sdk (package (name "ngs-sdk") - (version "1.2.5") + (version "1.3.0") (source (origin (method url-fetch) @@ -4393,7 +4396,7 @@ Roche 454, Ion Torrent and Pacific BioSciences SMRT.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "04y1fsmdnb5y86m3gg6f5g9wcscr6r25n7m8mdlcxy0i2q6w6cia")))) + "1wiyf4c6nm2j87pv015cbi0qny5byf3pbvcw3likifz5dl56ag40")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported @@ -4447,7 +4450,7 @@ simultaneously.") (define-public ncbi-vdb (package (name "ncbi-vdb") - (version "2.7.0") + (version "2.8.2") (source (origin (method url-fetch) @@ -4457,67 +4460,77 @@ simultaneously.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0x1cg1x8vy0yjlkp0snc1533zcjhxqzqsaiwqk598n7vvw37n8lf")))) + "1acn4bv81mfl137qnbn9995mjjhwd36pm0b7qli1iw5skrxa9j8m")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target #:phases - (alist-replace - 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; Override include path for libmagic - (substitute* "setup/package.prl" - (("name => 'magic', Include => '/usr/include'") - (string-append "name=> 'magic', Include => '" - (assoc-ref inputs "libmagic") - "/include" "'"))) - - ;; Install kdf5 library (needed by sra-tools) - (substitute* "build/Makefile.install" - (("LIBRARIES_TO_INSTALL =") - "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) - - (substitute* "build/Makefile.env" - (("CFLAGS =" prefix) - (string-append prefix "-msse2 "))) - - ;; The 'configure' script doesn't recognize things like - ;; '--enable-fast-install'. - (zero? (system* - "./configure" - (string-append "--build-prefix=" (getcwd) "/build") - (string-append "--prefix=" (assoc-ref outputs "out")) - (string-append "--debug") - (string-append "--with-xml2-prefix=" - (assoc-ref inputs "libxml2")) - (string-append "--with-ngs-sdk-prefix=" - (assoc-ref inputs "ngs-sdk")) - (string-append "--with-ngs-java-prefix=" - (assoc-ref inputs "java-ngs")) - (string-append "--with-hdf5-prefix=" - (assoc-ref inputs "hdf5")))))) - (alist-cons-after - 'install 'install-interfaces - (lambda* (#:key outputs #:allow-other-keys) - ;; Install interface libraries. On i686 the interface libraries - ;; are installed to "linux/gcc/i386", so we need to use the Linux - ;; architecture name ("i386") instead of the target system prefix - ;; ("i686"). - (mkdir (string-append (assoc-ref outputs "out") "/ilib")) - (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" - ,(system->linux-architecture - (or (%current-target-system) - (%current-system))) - "/rel/ilib") - (string-append (assoc-ref outputs "out") - "/ilib")) - ;; Install interface headers - (copy-recursively "interfaces" - (string-append (assoc-ref outputs "out") - "/include"))) - %standard-phases)))) + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + ;; Override include path for libmagic + (substitute* "setup/package.prl" + (("name => 'magic', Include => '/usr/include'") + (string-append "name=> 'magic', Include => '" + (assoc-ref inputs "libmagic") + "/include" "'"))) + + ;; Install kdf5 library (needed by sra-tools) + (substitute* "build/Makefile.install" + (("LIBRARIES_TO_INSTALL =") + "LIBRARIES_TO_INSTALL = kdf5.$(VERSION_LIBX) kdf5.$(VERSION_SHLX)")) + + (substitute* "build/Makefile.env" + (("CFLAGS =" prefix) + (string-append prefix "-msse2 "))) + + ;; Override search path for ngs-java + (substitute* "setup/package.prl" + (("/usr/local/ngs/ngs-java") + (assoc-ref inputs "java-ngs"))) + + ;; The 'configure' script doesn't recognize things like + ;; '--enable-fast-install'. + (zero? (system* + "./configure" + (string-append "--build-prefix=" (getcwd) "/build") + (string-append "--prefix=" (assoc-ref outputs "out")) + (string-append "--debug") + (string-append "--with-xml2-prefix=" + (assoc-ref inputs "libxml2")) + (string-append "--with-ngs-sdk-prefix=" + (assoc-ref inputs "ngs-sdk")) + (string-append "--with-hdf5-prefix=" + (assoc-ref inputs "hdf5"))))))) + (add-after 'install 'install-interfaces + (lambda* (#:key outputs #:allow-other-keys) + ;; Install interface libraries. On i686 the interface libraries + ;; are installed to "linux/gcc/i386", so we need to use the Linux + ;; architecture name ("i386") instead of the target system prefix + ;; ("i686"). + (mkdir (string-append (assoc-ref outputs "out") "/ilib")) + (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/" + ,(system->linux-architecture + (or (%current-target-system) + (%current-system))) + "/rel/ilib") + (string-append (assoc-ref outputs "out") + "/ilib")) + ;; Install interface headers + (copy-recursively "interfaces" + (string-append (assoc-ref outputs "out") + "/include")) + #t)) + ;; These files are needed by sra-tools. + (add-after 'install 'install-configuration-files + (lambda* (#:key outputs #:allow-other-keys) + (let ((target (string-append (assoc-ref outputs "out") "/kfg"))) + (mkdir target) + (install-file "libs/kfg/default.kfg" target) + (install-file "libs/kfg/certs.kfg" target)) + #t))))) (inputs `(("libxml2" ,libxml2) ("ngs-sdk" ,ngs-sdk) @@ -4728,7 +4741,7 @@ sequence itself can be retrieved from these databases.") (define-public sra-tools (package (name "sra-tools") - (version "2.7.0") + (version "2.8.2-1") (source (origin (method url-fetch) @@ -4738,13 +4751,19 @@ sequence itself can be retrieved from these databases.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "13paw7bq6y47d2pl0ac5gpgcqp1xsy1g7v1fwysm3hr8lb2dck17")))) + "1camsijmvv2s45mb4iyf44ghl4gkd4rl0viphpcgl3ccchy32a0g")))) (build-system gnu-build-system) (arguments `(#:parallel-build? #f ; not supported #:tests? #f ; no "check" target #:make-flags - (list (string-append "VDB_LIBDIR=" + (list (string-append "DEFAULT_CRT=" + (assoc-ref %build-inputs "ncbi-vdb") + "/kfg/certs.kfg") + (string-append "DEFAULT_KFG=" + (assoc-ref %build-inputs "ncbi-vdb") + "/kfg/default.kfg") + (string-append "VDB_LIBDIR=" (assoc-ref %build-inputs "ncbi-vdb") ,(if (string-prefix? "x86_64" (or (%current-target-system) @@ -5337,6 +5356,7 @@ information as possible.") (propagated-inputs `(("r-cluster" ,r-cluster) ("r-lattice" ,r-lattice) + ("r-mass" ,r-mass) ("r-mgcv" ,r-mgcv) ("r-permute" ,r-permute))) (home-page "https://cran.r-project.org/web/packages/vegan") @@ -5418,7 +5438,8 @@ microarrays.") `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) - ("r-s4vectors" ,r-s4vectors))) + ("r-s4vectors" ,r-s4vectors) + ("r-survival" ,r-survival))) (home-page "http://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") (description @@ -5716,6 +5737,7 @@ annotation infrastructure.") ("r-genomicalignments" ,r-genomicalignments) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) ("r-rtracklayer" ,r-rtracklayer) ("r-s4vectors" ,r-s4vectors))) (home-page "https://github.com/Kraus-Lab/groHMM") @@ -6115,7 +6137,8 @@ functionality.") (native-inputs `(("which" ,which))) (propagated-inputs - `(("r-graph" ,r-graph) + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) ("r-knitr" ,r-knitr) ("r-httr" ,r-httr) ("r-optparse" ,r-optparse) @@ -6643,6 +6666,7 @@ files.") ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicranges" ,r-genomicranges) ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) ("r-s4vectors" ,r-s4vectors))) (home-page "http://bioconductor.org/packages/SummarizedExperiment") (synopsis "Container for representing genomic ranges by sample") @@ -6834,8 +6858,9 @@ information about the latest version of the Gene Ontologies.") ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-go-db" ,r-go-db) - ("r-matrixstats" ,r-matrixstats) ("r-graph" ,r-graph) + ("r-lattice" ,r-lattice) + ("r-matrixstats" ,r-matrixstats) ("r-sparsem" ,r-sparsem))) (home-page "http://bioconductor.org/packages/topGO") (synopsis "Enrichment analysis for gene ontology") @@ -7611,9 +7636,9 @@ library implementing most of the pipeline's features.") `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) #t))))) (inputs - `(("r" ,r) + `(("r-minimal" ,r-minimal) ("r-rcas" ,r-rcas) - ("guile-next" ,guile-next) + ("guile-next" ,guile-2.2) ("guile-json" ,guile2.2-json) ("guile-redis" ,guile2.2-redis))) (native-inputs @@ -8227,7 +8252,8 @@ number detection tools.") "1wc1fjm6dzlsqqagm43y57w8jh8nsh0r0m8z1p6ximcb5gxqh7hn")))) (build-system r-build-system) (propagated-inputs - `(("r-genefilter" ,r-genefilter))) + `(("r-genefilter" ,r-genefilter) + ("r-mgcv" ,r-mgcv))) (home-page "http://bioconductor.org/packages/sva") (synopsis "Surrogate variable analysis") (description @@ -8279,6 +8305,7 @@ data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.") (propagated-inputs `(("r-seqminer" ,r-seqminer) ("r-mvtnorm" ,r-mvtnorm) + ("r-mass" ,r-mass) ("r-compquadform" ,r-compquadform) ("r-getopt" ,r-getopt))) (home-page "http://genome.sph.umich.edu/wiki/RareMETALS2") @@ -8437,6 +8464,7 @@ analysis.") `(("r-affy" ,r-affy) ("r-biobase" ,r-biobase) ("r-ggplot2" ,r-ggplot2) + ("r-lattice" ,r-lattice) ("r-limma" ,r-limma))) (home-page "http://bioconductor.org/packages/release/bioc/html/vsn.html") (synopsis "Variance stabilization and calibration for microarray data") @@ -8500,6 +8528,7 @@ specific parser.") (propagated-inputs `(("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-mass" ,r-mass) ("r-rcpp" ,r-rcpp))) (home-page "https://github.com/hredestig/pcamethods") (synopsis "Collection of PCA methods") @@ -8593,6 +8622,85 @@ contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.") (license license:artistic2.0))) +(define-public r-seurat + ;; Source releases are only made for new x.0 versions. All newer versions + ;; are only released as pre-built binaries. At the time of this writing the + ;; latest binary release is 1.4.0.12, which is equivalent to this commit. + (let ((commit "fccb77d1452c35ee47e47ebf8e87bddb59f3b08d") + (revision "1")) + (package + (name "r-seurat") + (version (string-append "1.4.0.12-" revision "." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/satijalab/seurat") + (commit commit))) + (file-name (string-append name "-" version "-checkout")) + (sha256 + (base32 + "101wq3aqrdmbfi3lqmq4iivk9iwbf10d4z216ss25hf7n9091cyl")) + ;; Delete pre-built jar. + (snippet + '(begin (delete-file "inst/java/ModularityOptimizer.jar") + #t)))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'build-jar + (lambda* (#:key inputs #:allow-other-keys) + (let ((classesdir "tmp-classes")) + (setenv "JAVA_HOME" (assoc-ref inputs "jdk")) + (mkdir classesdir) + (and (zero? (apply system* `("javac" "-d" ,classesdir + ,@(find-files "java" "\\.java$")))) + (zero? (system* "jar" + "-cf" "inst/java/ModularityOptimizer.jar" + "-C" classesdir "."))))))))) + (native-inputs + `(("jdk" ,icedtea "jdk"))) + (propagated-inputs + `(("r-ape" ,r-ape) + ("r-caret" ,r-caret) + ("r-cowplot" ,r-cowplot) + ("r-dplyr" ,r-dplyr) + ("r-fastica" ,r-fastica) + ("r-fnn" ,r-fnn) + ("r-fpc" ,r-fpc) + ("r-gdata" ,r-gdata) + ("r-ggplot2" ,r-ggplot2) + ("r-gplots" ,r-gplots) + ("r-gridextra" ,r-gridextra) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-lars" ,r-lars) + ("r-mixtools" ,r-mixtools) + ("r-pbapply" ,r-pbapply) + ("r-plyr" ,r-plyr) + ("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) + ("r-rtsne" ,r-rtsne) + ("r-stringr" ,r-stringr) + ("r-tclust" ,r-tclust) + ("r-tsne" ,r-tsne) + ("r-vgam" ,r-vgam))) + (home-page "http://www.satijalab.org/seurat") + (synopsis "Seurat is an R toolkit for single cell genomics") + (description + "This package is an R package designed for QC, analysis, and +exploration of single cell RNA-seq data. It easily enables widely-used +analytical techniques, including the identification of highly variable genes, +dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering +algorithms; density clustering, hierarchical clustering, k-means, and the +discovery of differentially expressed genes and markers.") + (license license:gpl3)))) + (define htslib-for-sambamba (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) (package |