diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 685 |
1 files changed, 180 insertions, 505 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 982cb7a984..26fcc3a41a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -84,6 +84,7 @@ #:use-module (gnu packages jemalloc) #:use-module (gnu packages dlang) #:use-module (gnu packages linux) + #:use-module (gnu packages lisp) #:use-module (gnu packages logging) #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) @@ -1091,7 +1092,7 @@ package provides command line tools using the Bio++ library.") (define-public blast+ (package (name "blast+") - (version "2.6.0") + (version "2.7.1") (source (origin (method url-fetch) (uri (string-append @@ -1099,8 +1100,7 @@ package provides command line tools using the Bio++ library.") version "/ncbi-blast-" version "+-src.tar.gz")) (sha256 (base32 - "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) - (patches (search-patches "blast+-fix-makefile.patch")) + "1jlq0afxxgczpp35k6mxh8mn4jzq7vqcnaixk166sfj10wq8v9qh")) (modules '((guix build utils))) (snippet '(begin @@ -1208,6 +1208,7 @@ package provides command line tools using the Bio++ library.") "include")) ; 33 MB (inputs `(("bzip2" ,bzip2) + ("lmdb" ,lmdb) ("zlib" ,zlib) ("pcre" ,pcre) ("perl" ,perl) @@ -1384,6 +1385,46 @@ gapped, local, and paired-end alignment modes.") (supported-systems '("x86_64-linux")) (license license:gpl3+))) +(define-public bowtie1 + (package + (name "bowtie1") + (version "1.2.2") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/bowtie-bio/bowtie/" + version "/bowtie-" version "-src.zip")) + (sha256 + (base32 + "1jl2cj9bz8lwz8dwnxbycn8yp8g4kky62fkcxifyf1ri0y6n2vc0")) + (modules '((guix build utils))) + (snippet + '(substitute* "Makefile" + ;; replace BUILD_HOST and BUILD_TIME for deterministic build + (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"") + (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; no "check" target + #:make-flags + (list "all" + (string-append "prefix=" (assoc-ref %outputs "out"))) + #:phases + (modify-phases %standard-phases + (delete 'configure)))) + (inputs + `(("tbb" ,tbb) + ("zlib" ,zlib))) + (supported-systems '("x86_64-linux")) + (home-page "http://bowtie-bio.sourceforge.net/index.shtml") + (synopsis "Fast aligner for short nucleotide sequence reads") + (description + "Bowtie is a fast, memory-efficient short read aligner. It aligns short +DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp +reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to +keep its memory footprint small: typically about 2.2 GB for the human +genome (2.9 GB for paired-end).") + (license license:artistic2.0))) + (define-public tophat (package (name "tophat") @@ -1729,7 +1770,9 @@ high-throughput sequencing data – with an emphasis on simplicity.") `(#:tests? #f ; there are no tests #:make-flags ;; Executables are copied directly to the PREFIX. - (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin")) + (list (string-append "PREFIX=" (assoc-ref %outputs "out") "/bin") + ;; Support longer sequences (e.g. Pacbio sequences) + "MAX_SEQ=60000000") #:phases (modify-phases %standard-phases ;; No "configure" script @@ -6240,6 +6283,48 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-scde + (package + (name "r-scde") + (version "1.99.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hms-dbmi/scde.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "10na2gyka24mszdxf92wz9h2c13hdf1ww30c68gfsw53lvvhhhxb")))) + (build-system r-build-system) + (propagated-inputs + `(("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-mgcv" ,r-mgcv) + ("r-rook" ,r-rook) + ("r-rjson" ,r-rjson) + ("r-cairo" ,r-cairo) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-edger" ,r-edger) + ("r-quantreg" ,r-quantreg) + ("r-nnet" ,r-nnet) + ("r-rmtstat" ,r-rmtstat) + ("r-extremes" ,r-extremes) + ("r-pcamethods" ,r-pcamethods) + ("r-biocparallel" ,r-biocparallel) + ("r-flexmix" ,r-flexmix))) + (home-page "https://hms-dbmi.github.io/scde/") + (synopsis "R package for analyzing single-cell RNA-seq data") + (description "The SCDE package implements a set of statistical methods for +analyzing single-cell RNA-seq data. SCDE fits individual error models for +single-cell RNA-seq measurements. These models can then be used for +assessment of differential expression between groups of cells, as well as +other types of analysis. The SCDE package also contains the pagoda framework +which applies pathway and gene set overdispersion analysis to identify aspects +of transcriptional heterogeneity among single cells.") + ;; See https://github.com/hms-dbmi/scde/issues/38 + (license license:gpl2))) + (define-public r-centipede (package (name "r-centipede") @@ -6264,54 +6349,6 @@ between two different types of motif instances using as much relevant information as possible.") (license (list license:gpl2+ license:gpl3+)))) -(define-public r-copynumber - (package - (name "r-copynumber") - (version "1.22.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "copynumber" version)) - (sha256 - (base32 - "0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3")))) - (build-system r-build-system) - (propagated-inputs - `(("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-genomicranges" ,r-genomicranges) - ("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/copynumber") - (synopsis "Segmentation of single- and multi-track copy number data") - (description - "This package segments single- and multi-track copy number data by a -penalized least squares regression method.") - (license license:artistic2.0))) - -(define-public r-geneplotter - (package - (name "r-geneplotter") - (version "1.60.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "geneplotter" version)) - (sha256 - (base32 - "10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz")))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-lattice" ,r-lattice) - ("r-rcolorbrewer" ,r-rcolorbrewer))) - (home-page "https://bioconductor.org/packages/geneplotter") - (synopsis "Graphics functions for genomic data") - (description - "This package provides functions for plotting genomic data.") - (license license:artistic2.0))) - (define-public r-genefilter (package (name "r-genefilter") @@ -6379,14 +6416,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.28.1") + (version "1.28.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0g5w9bn2nb3m670hkcsnhfvvkza2318z9irlhhwhb3n8rdzlsdym")))) + "134znafy7hn38rp4nia4pglz56fz6nbkxrf7z2k1sajfsgxa1hs6")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6674,38 +6711,6 @@ annotation infrastructure.") "This package provides a pipeline for the analysis of GRO-seq data.") (license license:gpl3+))) -(define-public r-txdb-hsapiens-ucsc-hg19-knowngene - (package - (name "r-txdb-hsapiens-ucsc-hg19-knowngene") - (version "3.2.2") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://bioconductor.org/packages/" - "release/data/annotation/src/contrib" - "/TxDb.Hsapiens.UCSC.hg19.knownGene_" - version ".tar.gz")) - (sha256 - (base32 - "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) - (properties - `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-genomicfeatures" ,r-genomicfeatures))) - (home-page - "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") - (synopsis "Annotation package for human genome in TxDb format") - (description - "This package provides an annotation database of Homo sapiens genome -data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" -track. The database is exposed as a @code{TxDb} object.") - (license license:artistic2.0))) - (define-public r-sparql (package (name "r-sparql") @@ -7127,28 +7132,6 @@ checks on R packages that are to be submitted to the Bioconductor repository.") that accept short and long options.") (license license:gpl2+))) -(define-public r-dnacopy - (package - (name "r-dnacopy") - (version "1.56.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "DNAcopy" version)) - (sha256 - (base32 - "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82")))) - (properties - `((upstream-name . "DNAcopy"))) - (build-system r-build-system) - (inputs - `(("gfortran" ,gfortran))) - (home-page "https://bioconductor.org/packages/DNAcopy") - (synopsis "Implementation of a circular binary segmentation algorithm") - (description "This package implements the circular binary segmentation (CBS) -algorithm to segment DNA copy number data and identify genomic regions with -abnormal copy number.") - (license license:gpl2+))) - (define-public r-s4vectors (package (name "r-s4vectors") @@ -7256,13 +7239,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.18.1") + (version "1.18.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s")))) + "07bm35jcczpyxap0b3gky4b28z38z423sngzsm19d9krjxr76b5p")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7312,13 +7295,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.28.10") + (version "1.28.11") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0kxf583cgkdz1shi85r0mpnfxmzi7s5f6srd1czbdl2iibvrm8jn")))) + "19bxi5b9fzqdjadb8bfm8xsgi6nvrwbgn1xcpk59bnmv9vzjkwrh")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7516,13 +7499,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.16.5") + (version "1.16.6") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1164dk0fajb2vrkfpcjs11055qf1cs4vvbnq0aqdaaf2p4lyx41l")))) + "1iv2xzm6lz371z0llhcxl8hmc5jfw0hjwnf1qc8d7jk9djgcaks2")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7567,13 +7550,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "01v4bjhj2i126pwyk0v9lvmfp2ih495xsq903k3xa2z24bjxphbi")))) + "02paq7klabdkaf1b8pmmbpmyqsj3yncnfsz62rgka6r4dpsilwk9")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7706,13 +7689,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.42.1") + (version "1.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6")))) + "1c76g6h9lx2nm7dvb2zp9dmrpk3vanx3zaz6q9clggpj7yj5lmjd")))) (build-system r-build-system) (arguments `(#:phases @@ -7753,13 +7736,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.34.2") + (version "1.34.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0qs94b0ywrjyc9m1jykrbch3lb07576m508dikvx18vwn304mban")))) + "09gc1vbqszrr3ixv4hsfan2l18fcf3gg58783mrfwjv6ci9c4w0d")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7878,37 +7861,6 @@ dependencies between GO terms can be implemented and applied.") genome data packages and support for efficient SNP representation.") (license license:artistic2.0))) -(define-public r-bsgenome-hsapiens-1000genomes-hs37d5 - (package - (name "r-bsgenome-hsapiens-1000genomes-hs37d5") - (version "0.99.1") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Hsapiens.1000genomes.hs37d5_" - version ".tar.gz")) - (sha256 - (base32 - "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) - (properties - `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") - (synopsis "Full genome sequences for Homo sapiens") - (description - "This package provides full genome sequences for Homo sapiens from -1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") - (license license:artistic2.0))) - (define-public r-impute (package (name "r-impute") @@ -8030,110 +7982,6 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) -(define-public r-org-hs-eg-db - (package - (name "r-org-hs-eg-db") - (version "3.7.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "org.Hs.eg.db_" version ".tar.gz")) - (sha256 - (base32 - "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) - (properties - `((upstream-name . "org.Hs.eg.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") - (synopsis "Genome wide annotation for Human") - (description - "This package contains genome-wide annotations for Human, primarily based -on mapping using Entrez Gene identifiers.") - (license license:artistic2.0))) - -(define-public r-org-ce-eg-db - (package - (name "r-org-ce-eg-db") - (version "3.7.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "org.Ce.eg.db_" version ".tar.gz")) - (sha256 - (base32 - "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) - (properties - `((upstream-name . "org.Ce.eg.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") - (synopsis "Genome wide annotation for Worm") - (description - "This package provides mappings from Entrez gene identifiers to various -annotations for the genome of the model worm Caenorhabditis elegans.") - (license license:artistic2.0))) - -(define-public r-org-dm-eg-db - (package - (name "r-org-dm-eg-db") - (version "3.7.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "org.Dm.eg.db_" version ".tar.gz")) - (sha256 - (base32 - "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) - (properties - `((upstream-name . "org.Dm.eg.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") - (synopsis "Genome wide annotation for Fly") - (description - "This package provides mappings from Entrez gene identifiers to various -annotations for the genome of the model fruit fly Drosophila melanogaster.") - (license license:artistic2.0))) - -(define-public r-org-mm-eg-db - (package - (name "r-org-mm-eg-db") - (version "3.7.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "org.Mm.eg.db_" version ".tar.gz")) - (sha256 - (base32 - "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) - (properties - `((upstream-name . "org.Mm.eg.db"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi))) - (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") - (synopsis "Genome wide annotation for Mouse") - (description - "This package provides mappings from Entrez gene identifiers to various -annotations for the genome of the model mouse Mus musculus.") - (license license:artistic2.0))) - (define-public r-seqlogo (package (name "r-seqlogo") @@ -8155,231 +8003,6 @@ plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).") (license license:lgpl2.0+))) -(define-public r-bsgenome-hsapiens-ucsc-hg19 - (package - (name "r-bsgenome-hsapiens-ucsc-hg19") - (version "1.4.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Hsapiens.UCSC.hg19_" - version ".tar.gz")) - (sha256 - (base32 - "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) - (properties - `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") - (synopsis "Full genome sequences for Homo sapiens") - (description - "This package provides full genome sequences for Homo sapiens as provided -by UCSC (hg19, February 2009) and stored in Biostrings objects.") - (license license:artistic2.0))) - -(define-public r-bsgenome-mmusculus-ucsc-mm9 - (package - (name "r-bsgenome-mmusculus-ucsc-mm9") - (version "1.4.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Mmusculus.UCSC.mm9_" - version ".tar.gz")) - (sha256 - (base32 - "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) - (properties - `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") - (synopsis "Full genome sequences for Mouse") - (description - "This package provides full genome sequences for Mus musculus (Mouse) as -provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") - (license license:artistic2.0))) - -(define-public r-bsgenome-mmusculus-ucsc-mm10 - (package - (name "r-bsgenome-mmusculus-ucsc-mm10") - (version "1.4.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Mmusculus.UCSC.mm10_" - version ".tar.gz")) - (sha256 - (base32 - "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) - (properties - `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") - (synopsis "Full genome sequences for Mouse") - (description - "This package provides full genome sequences for Mus -musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored -in Biostrings objects.") - (license license:artistic2.0))) - -(define-public r-txdb-mmusculus-ucsc-mm10-knowngene - (package - (name "r-txdb-mmusculus-ucsc-mm10-knowngene") - (version "3.4.4") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "TxDb.Mmusculus.UCSC.mm10.knownGene_" - version ".tar.gz")) - (sha256 - (base32 - "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) - (properties - `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-annotationdbi" ,r-annotationdbi))) - (home-page - "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") - (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") - (description - "This package loads a TxDb object, which is an R interface to -prefabricated databases contained in this package. This package provides -the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) -based on the knownGene track.") - (license license:artistic2.0))) - -(define-public r-bsgenome-celegans-ucsc-ce6 - (package - (name "r-bsgenome-celegans-ucsc-ce6") - (version "1.4.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Celegans.UCSC.ce6_" - version ".tar.gz")) - (sha256 - (base32 - "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) - (properties - `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") - (synopsis "Full genome sequences for Worm") - (description - "This package provides full genome sequences for Caenorhabditis -elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings -objects.") - (license license:artistic2.0))) - -(define-public r-bsgenome-celegans-ucsc-ce10 - (package - (name "r-bsgenome-celegans-ucsc-ce10") - (version "1.4.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Celegans.UCSC.ce10_" - version ".tar.gz")) - (sha256 - (base32 - "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) - (properties - `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") - (synopsis "Full genome sequences for Worm") - (description - "This package provides full genome sequences for Caenorhabditis -elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings -objects.") - (license license:artistic2.0))) - -(define-public r-bsgenome-dmelanogaster-ucsc-dm3 - (package - (name "r-bsgenome-dmelanogaster-ucsc-dm3") - (version "1.4.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://www.bioconductor.org/packages/" - "release/data/annotation/src/contrib/" - "BSgenome.Dmelanogaster.UCSC.dm3_" - version ".tar.gz")) - (sha256 - (base32 - "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) - (properties - `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) - (build-system r-build-system) - ;; As this package provides little more than a very large data file it - ;; doesn't make sense to build substitutes. - (arguments `(#:substitutable? #f)) - (propagated-inputs - `(("r-bsgenome" ,r-bsgenome))) - (home-page - "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") - (synopsis "Full genome sequences for Fly") - (description - "This package provides full genome sequences for Drosophila -melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in -Biostrings objects.") - (license license:artistic2.0))) - (define-public r-motifrg (package (name "r-motifrg") @@ -8477,14 +8100,14 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn")))) + "13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) (propagated-inputs @@ -9425,14 +9048,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.16.1") + (version "2.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0mlwg646k49klxrznckzfv54a9mz6irj42fqpaaa0xjm6cw2lwaa")) + "19fn58zl59kd0hsjjc6y975y9187nfls0028a4k3v0s9wfg5b3vn")) (modules '((guix build utils))) (snippet '(begin @@ -9453,7 +9076,8 @@ proteomics packages.") -lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n"))) #t))))) (inputs - `(("boost" ,boost) ; use this instead of the bundled boost sources + `(;; XXX Boost 1.69 will not work here. + ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9889,14 +9513,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.14.2") + (version "2.14.4") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "17fgrvcnbii9siv5rq5j09bxhqffx47f6jf10418qvr7hh61ic1g")))) + "18v2mk395svq3c19wzi6bjwjfnmrvjqkzmj7cmaji7rx4xdgz6ck")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10099,14 +9723,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.6.3") + (version "2.6.7") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0kzdsfk6mdwlp57sw4j2cf7lx5nc67v5j0xr3iag9kzmgikaq1lb")))) + "1wqq0m1fgvgkzq5zr2s9cj2s7qkg9lx3dwwsqixzs5fn52p4dn7f")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10511,14 +10135,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.26.4") + (version "1.26.5") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0jvcivgw0ahv2rjadxmrww76xambhf7silczmh38nn4yn4qw6w9y")))) + "1dpkcaar7qgzg3vgafvkplprhwmhzpb7ph009kr6ajm36hx4z81c")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -11613,7 +11237,7 @@ Browser.") (define-public bismark (package (name "bismark") - (version "0.19.1") + (version "0.20.1") (source (origin (method git-fetch) @@ -11623,18 +11247,25 @@ Browser.") (file-name (string-append name "-" version "-checkout")) (sha256 (base32 - "0yb5l36slwg02fp4b1jdlplgljcsxgqfzvzihzdnphd87dghcc84")) - (snippet - '(begin - ;; highcharts.js is non-free software. The code is available under - ;; CC-BY-NC or proprietary licenses only. - (delete-file "bismark_sitrep/highcharts.js") - #t)))) + "0xchm3rgilj6vfjnyzfzzymfd7djr64sbrmrvs3njbwi66jqbzw9")))) (build-system perl-build-system) (arguments `(#:tests? #f ; there are no tests + #:modules ((guix build utils) + (ice-9 popen) + (srfi srfi-26) + (guix build perl-build-system)) #:phases (modify-phases %standard-phases + ;; The bundled plotly.js is minified. + (add-after 'unpack 'replace-plotly.js + (lambda* (#:key inputs #:allow-other-keys) + (let* ((file (assoc-ref inputs "plotly.js")) + (installed "plotly/plotly.js")) + (let ((minified (open-pipe* OPEN_READ "uglify-js" file))) + (call-with-output-file installed + (cut dump-port minified <>)))) + #t)) (delete 'configure) (delete 'build) (replace 'install @@ -11653,10 +11284,11 @@ Browser.") "deduplicate_bismark" "filter_non_conversion" "bam2nuc" - "bismark2summary"))) + "bismark2summary" + "NOMe_filtering"))) (substitute* "bismark2report" - (("\\$RealBin/bismark_sitrep") - (string-append share "/bismark_sitrep"))) + (("\\$RealBin/plotly") + (string-append share "/plotly"))) (mkdir-p share) (mkdir-p docdir) (mkdir-p bin) @@ -11665,8 +11297,8 @@ Browser.") (for-each (lambda (file) (install-file file docdir)) docs) (copy-recursively "Docs/Images" (string-append docdir "/Images")) - (copy-recursively "bismark_sitrep" - (string-append share "/bismark_sitrep")) + (copy-recursively "plotly" + (string-append share "/plotly")) ;; Fix references to gunzip (substitute* (map (lambda (file) @@ -11677,7 +11309,18 @@ Browser.") "/bin/gunzip -c"))) #t)))))) (inputs - `(("gzip" ,gzip))) + `(("gzip" ,gzip) + ("perl-carp" ,perl-carp) + ("perl-getopt-long" ,perl-getopt-long))) + (native-inputs + `(("plotly.js" + ,(origin + (method url-fetch) + (uri (string-append "https://raw.githubusercontent.com/plotly/plotly.js/" + "v1.39.4/dist/plotly.js")) + (sha256 + (base32 "138mwsr4nf5qif4mrxx286mpnagxd1xwl6k8aidrjgknaqg88zyr")))) + ("uglify-js" ,uglify-js))) (home-page "http://www.bioinformatics.babraham.ac.uk/projects/bismark/") (synopsis "Map bisulfite treated sequence reads and analyze methylation") (description "Bismark is a program to map bisulfite treated sequencing @@ -13135,6 +12778,38 @@ descriptive settings file. The result is a set of comprehensive, interactive HTML reports with interesting findings about your samples.") (license license:gpl3+))) +(define-public genrich + (package + (name "genrich") + (version "0.5") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jsh58/Genrich.git") + (commit (string-append "v" version)))) + (sha256 + (base32 + "0x0q6z0208n3cxzqjla4rgjqpyqgwpmz27852lcvzkzaigymq4zp")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (install-file "Genrich" (string-append (assoc-ref outputs "out") "/bin")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (home-page "https://github.com/jsh58/Genrich") + (synopsis "Detecting sites of genomic enrichment") + (description "Genrich is a peak-caller for genomic enrichment +assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated +following the assay and produces a file detailing peaks of significant +enrichment.") + (license license:expat))) + (define-public mantis (let ((commit "4ffd171632c2cb0056a86d709dfd2bf21bc69b84") (revision "1")) |