diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 539 |
1 files changed, 324 insertions, 215 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bdb3ff761b..b7b1777c24 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,9 +11,10 @@ ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> -;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> +;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1615,7 +1616,7 @@ genome (2.9 GB for paired-end).") #t)))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ; not supported + '(#:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-samtools @@ -1639,16 +1640,18 @@ genome (2.9 GB for paired-end).") (("#include <bam.h>") "#include <samtools/bam.h>") (("#include <sam.h>") "#include <samtools/sam.h>")) #t))))) + (native-inputs + `(("gcc" ,gcc-5))) ;; doesn't build with later versions (inputs `(("boost" ,boost) ("bowtie" ,bowtie) - ("samtools" ,samtools-0.1) ("ncurses" ,ncurses) - ("python" ,python-2) ("perl" ,perl) - ("zlib" ,zlib) - ("seqan" ,seqan-1))) - (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + ("python" ,python-2) + ("samtools" ,samtools-0.1) + ("seqan" ,seqan-1) + ("zlib" ,zlib))) + (home-page "https://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description "TopHat is a fast splice junction mapper for nucleotide sequence @@ -2995,7 +2998,8 @@ reasonable amount of time and memory. For large alignments, FastTree is (inputs `(("libgtextutils" ,libgtextutils))) (native-inputs - `(("pkg-config" ,pkg-config))) + `(("gcc" ,gcc-6) ;; doesn't build with later versions + ("pkg-config" ,pkg-config))) (home-page "http://hannonlab.cshl.edu/fastx_toolkit/") (synopsis "Tools for FASTA/FASTQ file preprocessing") (description @@ -6669,14 +6673,14 @@ information as possible.") (define-public r-genefilter (package (name "r-genefilter") - (version "1.66.0") + (version "1.68.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genefilter" version)) (sha256 (base32 - "1jq7lam4dnbvz55lx93kcl9afl8xfjd6xs374d35m21bkay418kj")))) + "1xjr02qhldspjwd6y374wgik18fgywb6408wsz471i8b4ik98ckc")))) (build-system r-build-system) (native-inputs `(("gfortran" ,gfortran))) @@ -6684,7 +6688,7 @@ information as possible.") `(("r-annotate" ,r-annotate) ("r-annotationdbi" ,r-annotationdbi) ("r-biobase" ,r-biobase) - ("r-s4vectors" ,r-s4vectors) + ("r-biocgenerics" ,r-biocgenerics) ("r-survival" ,r-survival))) (home-page "https://bioconductor.org/packages/genefilter") (synopsis "Filter genes from high-throughput experiments") @@ -6696,14 +6700,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.24.0") + (version "1.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "0fkk326addm2cw688gnmdzsmri5qx8j6ldnr4xin6kjnwicqhlqd")))) + "1lmbhznfs8dz9ipd53z4ccwvwxqwzx1ayw56jlrvlsambaj8fash")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6733,14 +6737,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "1b2s0vwm97g0wgm4ms0f4pqkqiqmxscnhg700aybl5vx0m2fa8xm")))) + "0sqqb65ckliif2nmvlvc7w49id59z0nvqcdz5gry8l2mn6azrf6a")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6776,14 +6780,14 @@ exploration of the results.") (define-public r-annotationforge (package (name "r-annotationforge") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationForge" version)) (sha256 (base32 - "0m4w8n2711wr28znv646cfc7m5jqlr8friz334zdyjmhg7m2xkb7")))) + "0h2r60v339ajk5r6xq4iwwcpihdvf12fi8255byr2dhglzrd8xl7")))) (properties `((upstream-name . "AnnotationForge"))) (build-system r-build-system) @@ -6806,14 +6810,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.60.0") + (version "1.62.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "06brn9hl6lybx6hdfp1sycwj6wn1bjfi8xyhpy0v122v1z8d5mbz")))) + "0ixbkdirf08i400db587r262j52sdwdgk3884nxk5xkbhx2m6vg0")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs @@ -6829,14 +6833,14 @@ the graph algorithms contained in the Boost library.") (define-public r-gseabase (package (name "r-gseabase") - (version "1.46.0") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GSEABase" version)) (sha256 (base32 - "0vh53xk2prjbdkbr3hwfiflx1gh7ilrqs3j1p3lyd6syy3rn9n83")))) + "0kcb90sxlf19d5dxhdbqk9x62svky4262cccl0wxarbq6gf3bd57")))) (properties `((upstream-name . "GSEABase"))) (build-system r-build-system) (propagated-inputs @@ -6856,14 +6860,14 @@ Enrichment Analysis} (GSEA).") (define-public r-category (package (name "r-category") - (version "2.50.0") + (version "2.52.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Category" version)) (sha256 (base32 - "1n36xfnwn2np5f0lix9abvv9w6jb25jqz3xzvqzklz9s1af4k6x4")))) + "0ga0ij9hyzsxa5pavwmv35i8xggia2wygrk4m4z8an0qcvgy3v5g")))) (properties `((upstream-name . "Category"))) (build-system r-build-system) (propagated-inputs @@ -6887,14 +6891,14 @@ analysis.") (define-public r-gostats (package (name "r-gostats") - (version "2.50.0") + (version "2.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GOstats" version)) (sha256 (base32 - "1a95i6awm2a8xv42fg2z3n29fg9z29i45kd80hxf6mvqqgzj80xp")))) + "19f4gxm3sbprqrnwzvskvywv6j4ibm8xkrbgg4h0fvh2b5331nwc")))) (properties `((upstream-name . "GOstats"))) (build-system r-build-system) (propagated-inputs @@ -6918,14 +6922,14 @@ testing and other simple calculations.") (define-public r-shortread (package (name "r-shortread") - (version "1.42.0") + (version "1.44.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ShortRead" version)) (sha256 (base32 - "1irqzdgsavjqsq0vva4966qh8qgn7xn9382dmhahm1hxb94qmi59")))) + "1dh3q83hmi4l72vpif6dn51dzbi9ljrjgkq2zxg4sqy2jxv4vwza")))) (properties `((upstream-name . "ShortRead"))) (build-system r-build-system) (inputs @@ -6960,14 +6964,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.18.2") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "18s5vpmw766pm64w7bwwfgpsv9yzhwclf0ya1rpqz8qslw7bbdjf")))) + "17r25v9wcglyma2v1c8fka80dm7fx86saxlsb2aprmwi4h3dhb0j")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7007,14 +7011,14 @@ annotation infrastructure.") (define-public r-grohmm (package (name "r-grohmm") - (version "1.18.0") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "groHMM" version)) (sha256 (base32 - "1p368qf8ab1vy8gl2j7rx0l7bvva4m7w06i364rqzs0sdyzlbm3y")))) + "0ywr8f6bfhg2ia3n4rmsxr4v1xqmlyhkwh0rvkgh3yqgnbvihndg")))) (properties `((upstream-name . "groHMM"))) (build-system r-build-system) (propagated-inputs @@ -7240,13 +7244,13 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.52.2") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0qwrsd9fcpkv7hhzy1scnj7ahdxi6cjary28kqk6b36gkzmnrw4r")))) + "0yn8jys1900d31haayz0ppqk5y79mwjajwp4alz6pln3dbs70f3g")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7268,13 +7272,13 @@ also known as views, in a controlled vocabulary.") (define-public r-biocstyle (package (name "r-biocstyle") - (version "2.12.0") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocStyle" version)) (sha256 (base32 - "029x8r9rcx6zy0xixdpwxai4jv4ynb161821fzac6z4r8k418398")))) + "0nc1cbzp5zdwc0rss4r6v7cpgynmmnj3sczwmajr58nabkndwsvf")))) (properties `((upstream-name . "BiocStyle"))) (build-system r-build-system) @@ -7294,13 +7298,13 @@ functionality.") (define-public r-bioccheck (package (name "r-bioccheck") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocCheck" version)) (sha256 (base32 - "1gkw9s6dhdryga9ap5yhvcqg9jsy4cn417ayqk1qiv6fy91fd124")))) + "1qnvl5yajgh67ijkq6gdsafri1k5hyw5gzn2ccqk9ymx6i2xd80g")))) (properties `((upstream-name . "BiocCheck"))) (build-system r-build-system) @@ -7341,13 +7345,13 @@ checks on R packages that are to be submitted to the Bioconductor repository.") (define-public r-s4vectors (package (name "r-s4vectors") - (version "0.22.1") + (version "0.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "S4Vectors" version)) (sha256 (base32 - "0cpxqb18wd3pjd7bi8lry13sm5ffqahcvvxpk5pwm5xcj30cdlm9")))) + "1rr7ml3gn83g8fbvhgvryyzlh4p3qgpwcrsz6ii4y7gh1hqxggpx")))) (properties `((upstream-name . "S4Vectors"))) (build-system r-build-system) @@ -7368,13 +7372,13 @@ S4Vectors package itself.") (define-public r-iranges (package (name "r-iranges") - (version "2.18.3") + (version "2.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "IRanges" version)) (sha256 (base32 - "05rw2b2bwns443n7d6lf97zdv1jbqdii2nprhs6x852w73m2a2g3")))) + "0qssp04wfrc1r92hd3szy03n8sdz8vrqjdxa2mcrsc0k0n9bchz5")))) (properties `((upstream-name . "IRanges"))) (build-system r-build-system) @@ -7420,13 +7424,13 @@ ID and species. It is used by functions in the GenomeInfoDb package.") (define-public r-genomeinfodb (package (name "r-genomeinfodb") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomeInfoDb" version)) (sha256 (base32 - "0zkhms81b3jz30q7ag81a1mq1rgqg4izyfdvcni68gvn8gm7kdyk")))) + "07zljs2mfi8rf31g903f43v2f7767xbnflfrx9qjnmgf7bm039x0")))) (properties `((upstream-name . "GenomeInfoDb"))) (build-system r-build-system) @@ -7448,13 +7452,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.8") + (version "3.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "1wwimzviy2vklp80faz7sbbp74qcw2csbmlfgvzj7b785vwarpwg")))) + "1m7l6fbyik1b79v0h9qkmpa39svij1yiw24gxahbdqjg7fzsavh3")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7476,13 +7480,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.30.1") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "144x3d3b9a3q5jy4aqrk1nf2yavwjhwlf71s7qyr4x3ms3wmvf8i")))) + "009s7rzp78s2w6iybizina42qx2w8qv3xwjbkpqphmm451maykgs")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7515,13 +7519,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.40.6") + (version "3.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8")))) + "0cfynv6qbnar5rl7vjh5lvddd381g9wqx1zd6a7l130hf59mwswn")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7534,13 +7538,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-xvector (package (name "r-xvector") - (version "0.24.0") + (version "0.26.0") (source (origin (method url-fetch) (uri (bioconductor-uri "XVector" version)) (sha256 (base32 - "12y09pwy86h1za6cmaxs960r7fs0vjzhl0li8jn59vqq9liza1ap")))) + "0s2gg84yzl5ffkzp6n7kh0jjk1vd90z189f5hkfn18rn67cy2nv7")))) (properties `((upstream-name . "XVector"))) (build-system r-build-system) @@ -7570,13 +7574,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.") (define-public r-genomicranges (package (name "r-genomicranges") - (version "1.36.1") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicRanges" version)) (sha256 (base32 - "1yid84gn0052v52h84685lvk854grl1wl65psmlmxx9yyykgc0jn")))) + "0xdds6ws7jjdfy4x3mb0qhy43kpxdmifmpw0jdk4wgw999zabb50")))) (properties `((upstream-name . "GenomicRanges"))) (build-system r-build-system) @@ -7599,13 +7603,13 @@ manipulating genomic intervals and variables defined along a genome.") (define-public r-biobase (package (name "r-biobase") - (version "2.44.0") + (version "2.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biobase" version)) (sha256 (base32 - "15yl92niqamx3lmwd11zlk0xniibqnh1gi280iadxicmchi83npc")))) + "1gx41083dqlm59vwqdxvc4ny31x91j48mda9n3scg0f2zwasvqgl")))) (properties `((upstream-name . "Biobase"))) (build-system r-build-system) @@ -7621,13 +7625,13 @@ on Bioconductor or which replace R functions.") (define-public r-annotationdbi (package (name "r-annotationdbi") - (version "1.46.1") + (version "1.48.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationDbi" version)) (sha256 (base32 - "13nanz4nzy0mcda8ljz2g8d81hpqfz6jky7ydz5hpk0g2264b9ga")))) + "09piz1f0xpbb4amskx4ilby6lfrn27hhwk75il2c4lq6m3hr4w8s")))) (properties `((upstream-name . "AnnotationDbi"))) (build-system r-build-system) @@ -7648,21 +7652,23 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.5") + (version "2.42.0") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1kjvxnkpsx3j2hji3cg3ka2gv8a9mg117lzzxyqjb7qa4zw7dipx")))) + "0difh4dsccjzhpfkvajy2adh98ym9164gd6clnsnic6qr6sk86ss")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) ("r-progress" ,r-progress) - ("r-rcurl" ,r-rcurl) + ("r-rappdirs" ,r-rappdirs) ("r-stringr" ,r-stringr) ("r-xml" ,r-xml))) (home-page "https://bioconductor.org/packages/biomaRt") @@ -7681,13 +7687,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.18.1") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3")))) + "0g0znb4whsvb9hpwx9xaasdi5n4vjqw8cpdyqgrdrjm91rls1h21")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7706,13 +7712,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.52.0") + (version "2.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "0inrl97hli3qz6cfxcikc4picmbrqc8phdgqi18ynlvxy5ql64h4")))) + "0pq7g2hflx2cjlpwdj6mscw9hnxvlf5y50dxf48lbrf9r3q9kmyp")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7732,13 +7738,13 @@ biological sequences or sets of sequences.") (define-public r-rsamtools (package (name "r-rsamtools") - (version "2.0.3") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "Rsamtools" version)) (sha256 (base32 - "03qfpaqbffirpnby88mv6h45njfapli28crdvg35h2zi2jkkmhvp")))) + "0hpdc88prpq1gcja89n5s1ndcg81523qrkbkm9gbhm7rm8wmi8cl")))) (properties `((upstream-name . "Rsamtools"))) (build-system r-build-system) @@ -7777,13 +7783,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.10.0") + (version "0.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "0l907ggxndn3f29zvsd5pppmp4c31rb22r6zkhvgph7xdxahyy6z")))) + "1yr4i2x127v814nxg53aibp77p3vg76f3n3hgknpwx3snfhc81xs")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) @@ -7809,13 +7815,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.14.1") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f")))) + "1z9bdk49dajafkfvv99nv6zyn6v70iyyy2jgdp5w5z8174a2bnn1")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) @@ -7840,13 +7846,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.20.1") + (version "1.22.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0s3q97q4pgj5jwn4g95al44rahrwsncsf45v01v4071msx3xmjxq")))) + "065xvy4pkda0ajvl1b75iski95k1pnbhxwdq7vkfl8v55915vqh6")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7873,13 +7879,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.44.4") + (version "1.46.0") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0dnifr58j2si2qbnvap2wslz3xgjv3h4l7a6v7nmmc57hq6kdbym")))) + "0lp9xsm8kqrgpwgwj7qaqcv1z6qynbz084grlpwp94zsp2ppf0n6")))) (build-system r-build-system) (arguments `(#:phases @@ -7920,13 +7926,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.4") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k")))) + "0xd9rlsicycbanbcfhc97cj8b8vk94g7lkbmhk37w1511bq35wz5")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) @@ -7985,13 +7991,13 @@ information about the latest version of the Gene Ontologies.") (define-public r-topgo (package (name "r-topgo") - (version "2.36.0") + (version "2.38.1") (source (origin (method url-fetch) (uri (bioconductor-uri "topGO" version)) (sha256 (base32 - "09z42jwz5vh289ijz3x68zv5vmgkgcbhlp73vvmna1gld5lh5kz1")))) + "1kw9m2j67895k58lx9msc248pjwblp8clxwgsl01cql7sgi1xzlf")))) (properties `((upstream-name . "topGO"))) (build-system r-build-system) @@ -8018,13 +8024,13 @@ dependencies between GO terms can be implemented and applied.") (define-public r-bsgenome (package (name "r-bsgenome") - (version "1.52.0") + (version "1.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "BSgenome" version)) (sha256 (base32 - "0zwx42s73hc1vhn0v82i67mcixdwwc6n6q5h5vpnhpxlm4qwgqzp")))) + "0nn1b3h4hmnx5whf2cmzmyxdrcf4myj8c38rwr0sw4rc07xfzndy")))) (properties `((upstream-name . "BSgenome"))) (build-system r-build-system) @@ -8048,13 +8054,13 @@ genome data packages and support for efficient SNP representation.") (define-public r-impute (package (name "r-impute") - (version "1.58.0") + (version "1.60.0") (source (origin (method url-fetch) (uri (bioconductor-uri "impute" version)) (sha256 (base32 - "144jb889979cv3il2zxqk724v3sj1wnzjm3lkspxcvk29dbb9q8j")))) + "0igz1phjd1j9bg9z4kyy7j8v9bxi9sdwz4df26r51i2vavlbrf4q")))) (native-inputs `(("gfortran" ,gfortran))) (build-system r-build-system) @@ -8068,13 +8074,13 @@ microarray data, using nearest neighbor averaging.") (define-public r-seqpattern (package (name "r-seqpattern") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqPattern" version)) (sha256 (base32 - "1ljqscbmrmi5d4lzzvg2d86sqzch26yxw57d33qyid300wm60db2")))) + "1gxrq6s2hiyac69idh5r1nbr1s69n0hg4ap2skm4g6857av9pwqf")))) (properties `((upstream-name . "seqPattern"))) (build-system r-build-system) @@ -8095,13 +8101,13 @@ reference point and sorted by a user defined feature.") (define-public r-genomation (package (name "r-genomation") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "genomation" version)) (sha256 (base32 - "06i711pwq9znd7plh0p25skxnnh5dyl61c33k9gma243wvlzmlkj")))) + "1sba928h23b67gr3i4yj1bg655g24l3bcgsf5gvymzrv5idrss1l")))) (build-system r-build-system) (propagated-inputs `(("r-biostrings" ,r-biostrings) @@ -8169,14 +8175,14 @@ downloaded from Encode.") (define-public r-seqlogo (package (name "r-seqlogo") - (version "1.50.0") + (version "1.52.0") (source (origin (method url-fetch) (uri (bioconductor-uri "seqLogo" version)) (sha256 (base32 - "1z63imr1a24nqijpvxaxlakykcsadfqyxl2b3vlllncxnjjvb52b")))) + "0s94aahp8ma1crmp83dz65ifjwrx6wqi3q6005lmbp8yk2x1rkj4")))) (properties `((upstream-name . "seqLogo"))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/seqLogo") @@ -8190,14 +8196,14 @@ Stephens (1990).") (define-public r-motifrg (package (name "r-motifrg") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "motifRG" version)) (sha256 (base32 - "02c7fbjwdq7pk96bd2rn07l9r2hqy00s3hfpli5ybmwgvc9h9z4z")))) + "0s6wdr036lra9x93r9k8wvicbkgzypjh3jp46h92yacw8d829k0d")))) (properties `((upstream-name . "motifRG"))) (build-system r-build-system) (propagated-inputs @@ -8271,13 +8277,13 @@ R/qtl, to better handle high-dimensional data and complex cross designs.") (define-public r-zlibbioc (package (name "r-zlibbioc") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "zlibbioc" version)) (sha256 (base32 - "1h0a2ps2rfk9azzps7p23sxj5z1giv8gcx0ypzgyz7fkr4xi9z7k")))) + "1xh7qan0w62mzsmanbx9vcj6ygdfhzw1abaxijkq7f4nh5w87idj")))) (properties `((upstream-name . "zlibbioc"))) (build-system r-build-system) @@ -8313,21 +8319,22 @@ secondary structure and comparative analysis in R.") (define-public r-rhtslib (package (name "r-rhtslib") - (version "1.16.3") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhtslib" version)) (sha256 (base32 - "1lmrfr32nrz36abn440kvzzck53y2320xjxqzs2jw7m2a9h3ryak")))) + "04inkq44lxwymqv51mxgaphasqjcdc9rl5p58imnrdm0kszs8prm")))) (properties `((upstream-name . "Rhtslib"))) (build-system r-build-system) ;; Without this a temporary directory ends up in the Rhtslib.so binary, ;; which makes R abort the build. (arguments '(#:configure-flags '("--no-staged-install"))) (propagated-inputs - `(("r-zlibbioc" ,r-zlibbioc))) + `(("curl" ,curl) + ("r-zlibbioc" ,r-zlibbioc))) (inputs `(("zlib" ,zlib))) (native-inputs @@ -8343,14 +8350,14 @@ of other R packages who wish to make use of HTSlib.") (define-public r-bamsignals (package (name "r-bamsignals") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "bamsignals" version)) (sha256 (base32 - "15q1q51dwl9qxfkf10yppw4m194ba03nq9plsrbj8fqj00v4729i")))) + "0699b0pqbs0dvs91yjibcjc90lxj9mg8rcml4a6wchfr9md7n74w")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8373,13 +8380,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.10.1") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz")))) + "1s3gvvxi1029d1vfwnjh21nnw3mlx08kcwz63891hml9y850cvsn")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs @@ -8474,14 +8481,14 @@ library implementing most of the pipeline's features.") (define-public r-mutationalpatterns (package (name "r-mutationalpatterns") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MutationalPatterns" version)) (sha256 (base32 - "1k3r06xj1nim1s8as1i7fykfa6fbb4x456kslbzdvbf83ppx34z3")))) + "08715l6swrlccviw7932v5hyrd2x4c6049vy9qnxk0lw3sp1zvsf")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8579,13 +8586,13 @@ factors bound at the specific regions.") (define-public r-tximport (package (name "r-tximport") - (version "1.12.3") + (version "1.14.0") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "070nx0blvvfhsnkbb5j899wy7dgalrh4xfcciir9l2xl67lna1zf")))) + "09r23n2812q89by0r0cz2fx1gfnmn3jb3hwbg61m52bika82pakj")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -8601,13 +8608,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.28.1") + (version "2.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "027cv1kh3xl66lrrahv2jgfmvgcwfpcj9dpgdj5fd9ybf5nyjcwb")))) + "18pv74jj4wr1981r92ss10qkgf5g1b09dsbz3im3j70a4l5l0df0")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -8628,13 +8635,13 @@ the available RAM.") (define-public r-annotationfilter (package (name "r-annotationfilter") - (version "1.8.0") + (version "1.10.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationFilter" version)) (sha256 (base32 - "15qh4jwxxqsnb308nxzj99gckfk18rhp8g26q1xwgkr57zc5kcrx")))) + "1l9sxhlvnwn6327vgg02h11ppmqr2zr07ff8wmcng0i1jbqwa8q5")))) (properties `((upstream-name . "AnnotationFilter"))) (build-system r-build-system) @@ -8933,14 +8940,14 @@ common bioinformatics tools.") (define-public r-chipseq (package (name "r-chipseq") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "chipseq" version)) (sha256 (base32 - "1835nhrxcaqpqf1kxrsk1js8bf7x33z1n3bqjvm8404091acqyma")))) + "1ln6bn08xig3j6ryak1xfkjhvpnlm2vf1czz9hlj6f02299nbs6l")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -8985,14 +8992,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.16.0") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0kv3k58wyyicq1hhq7bddh0v3b2ksz6fa47skvnp8f193csza9g6")))) + "0llg1zpxg7qnvja5f5w1z1xic0jdg6zc4mfn97h2sm44skxxcyl1")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9025,13 +9032,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "1z687vpi5kwcqpnd6r74c5y72hcsbqlwg0bk95kksgpi81q710qj")))) + "0klwc0sbmrxj1lxbz16pl39rxjm0pi57gjw547hlgnac1p9fspzy")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9072,14 +9079,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.32.1") + (version "3.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "0jj6klfha5v5qmx2sjblf1an6s2zqd7mmgsp7sfmh4k2jpqi3jm9")))) + "1bzms6idx30s4nxl610zwa8rjxsyxb5pf3vxsdfmxg8j4pab9gh1")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -9182,14 +9189,14 @@ as allowing spectra with different resolutions.") (define-public r-protgenerics (package (name "r-protgenerics") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ProtGenerics" version)) (sha256 (base32 - "12jjwmg58b4xbivxlw4pffq0qfi2c1c5hyrci0sfyphrc99fvx0i")))) + "1k1ggjgx2la8b21841a4ngkp6xfxwz0czv7x960r7i1jqif8y48z")))) (properties `((upstream-name . "ProtGenerics"))) (build-system r-build-system) (home-page "https://github.com/lgatto/ProtGenerics") @@ -9202,14 +9209,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.18.1") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "1pr1pcrg3r3pccm5ag6l8ic6rpqbk9jnlb9mm7g4ak5jwrajbzjq")) + "1cwd7phlc5jbx6r6cznyfbdpvcin5fvsaasbbi65zn0s92a80r13")) (modules '((guix build utils))) (snippet '(begin @@ -9231,7 +9238,7 @@ proteomics packages.") #t))))) (inputs `(;; Our default boost package won't work here, unfortunately, even with - ;; mzR version 2.18.1. + ;; mzR version 2.20.0. ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources ("zlib" ,zlib))) (propagated-inputs @@ -9256,14 +9263,14 @@ previously been used in XCMS.") (define-public r-affyio (package (name "r-affyio") - (version "1.54.0") + (version "1.56.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affyio" version)) (sha256 (base32 - "1s78hm51fgac3i2j4bbdy0z6g14370154s6km8lldc9zpahx8b6p")))) + "0sbkadxdlx7qzxc8z8iv90y6j9b2f62mk3i54dijjh56x3hjy3hb")))) (build-system r-build-system) (propagated-inputs `(("r-zlibbioc" ,r-zlibbioc))) @@ -9280,14 +9287,14 @@ CDF file formats.") (define-public r-affy (package (name "r-affy") - (version "1.62.0") + (version "1.64.0") (source (origin (method url-fetch) (uri (bioconductor-uri "affy" version)) (sha256 (base32 - "05vz0vf3472s1ivfhc0gc8yz98y4rvvp7cf6kfbxhy1b23im1bgk")))) + "131za66wbaz9y86gvjqcc2yd1f2ngl2b796xw726g75djhdgxgap")))) (build-system r-build-system) (propagated-inputs `(("r-affyio" ,r-affyio) @@ -9308,14 +9315,14 @@ analysis.") (define-public r-vsn (package (name "r-vsn") - (version "3.52.0") + (version "3.54.0") (source (origin (method url-fetch) (uri (bioconductor-uri "vsn" version)) (sha256 (base32 - "1vqmyxg06kgq9m3w6n0jykqm4jgsjw879r4s216wlcq4xc94dh1r")))) + "1naqzb2m0km8fzr6chf9z71sisrwviy1fdi9b3hn4i8p18b4kqzh")))) (build-system r-build-system) (propagated-inputs `(("r-affy" ,r-affy) @@ -9342,14 +9349,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "0vnyg7jlmy7ain7gmjwhqyqr664znrvrdlh7zd63563vhb87qarn")))) + "1glcv096bn6pxlw89dlij1nzpwnjvrbxysvw2gm6qgm7rhxlaxrw")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9372,14 +9379,14 @@ specific parser.") (define-public r-pcamethods (package (name "r-pcamethods") - (version "1.76.0") + (version "1.78.0") (source (origin (method url-fetch) (uri (bioconductor-uri "pcaMethods" version)) (sha256 (base32 - "0svf4n7l0afy4wwgs6x8x4dm330r3311l5vmsxw2f0r4axkh3bzk")))) + "1wir67kfjm0m9gf0ki8qmvh45n4gx2k0wfl9pd1hp4g62fbrj1pj")))) (properties `((upstream-name . "pcaMethods"))) (build-system r-build-system) (propagated-inputs @@ -9402,14 +9409,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.10.1") + (version "2.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0z63yqazkycq0zbbarq9ida6al35hv3g7g9g7s7bss4gh0hk7lhd")))) + "1z889xkfphqqmv31i8hh5xqyclv660ic26rfck5bjpgk3s2zzwi6")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9445,14 +9452,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.18.1") + (version "1.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb")))) + "0m71f2y12hmwvng45kzz4r4qrgc2jbd7j9gprmw8y5laawpdaifg")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9484,13 +9491,13 @@ and irregular enzymatic cleavages, mass measurement accuracy, etc.") (define-public r-seurat (package (name "r-seurat") - (version "3.1.1") + (version "3.1.2") (source (origin (method url-fetch) (uri (cran-uri "Seurat" version)) (sha256 (base32 - "084lr2fjdksshsmv1ww82bgn3a9mml7kswsidjrs89snabgvn360")))) + "0m1qi39snbmkkv1p07bzg1r7snc9x6a1y0dghvpk1nzgcfpmnsj4")))) (properties `((upstream-name . "Seurat"))) (build-system r-build-system) (propagated-inputs @@ -9546,14 +9553,14 @@ discovery of differentially expressed genes and markers.") (define-public r-aroma-light (package (name "r-aroma-light") - (version "3.14.0") + (version "3.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "aroma.light" version)) (sha256 (base32 - "0a1prl4jhbqpa85i2vyia1ks9iippzl8np50fvm9wx8kbjxna5l6")))) + "0cgdg650j4dl0b45pwaw49ib97dwjazrv9sqzkygrjmcnnfxry8x")))) (properties `((upstream-name . "aroma.light"))) (build-system r-build-system) (propagated-inputs @@ -9573,14 +9580,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.36.0") + (version "1.38.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "0jppqrikg9qfqcfw5qd3m5c7bag9g23bc0kcpk5zfkk1wv09mnlm")))) + "14pys93gsl50xmq5pc7pp1g20v3ywlg0yzkkhwb3kiy8573xn9nc")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9604,14 +9611,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.18.0") + (version "2.20.0") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "0mmc9bij17w4mfwcc566zbj5fvqgl8gfqs0qvj6ri4mbcql9jxb3")))) + "19mgzbv8yxgvw86wpq401l27q55ygawlngl775yavwccz1zbhjnj")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9643,14 +9650,14 @@ global-scaling and full-quantile normalization.") (define-public r-interactivedisplaybase (package (name "r-interactivedisplaybase") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "interactiveDisplayBase" version)) (sha256 (base32 - "1kkyv7hkygacmksvld9gs3ycf6wlblqcwi11nny0hq3l0ha265v5")))) + "0zwf3ma6wf4zypl6bgjp0n72k2hmp0g16gzl4v3y4157rxcbpl0n")))) (properties `((upstream-name . "interactiveDisplayBase"))) (build-system r-build-system) @@ -9667,14 +9674,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "0c773cmhng907839f0bq161jky7362lxxny36ac55qxiz1giqi8j")))) + "19vj3bk8jz68q84g3j8xs1s9bqz90lbwbciig1h45zvn2zc6087m")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -9682,6 +9689,7 @@ Shiny-based display methods for Bioconductor objects.") ("r-biocfilecache" ,r-biocfilecache) ("r-biocgenerics" ,r-biocgenerics) ("r-biocmanager" ,r-biocmanager) + ("r-biocversion" ,r-biocversion) ("r-curl" ,r-curl) ("r-dplyr" ,r-dplyr) ("r-httr" ,r-httr) @@ -9705,14 +9713,14 @@ by the user, helping with quick and reproducible access.") (define-public r-fastseg (package (name "r-fastseg") - (version "1.30.0") + (version "1.32.0") (source (origin (method url-fetch) (uri (bioconductor-uri "fastseg" version)) (sha256 (base32 - "03gggz29nf8kyy9clkifqr0xm8v0yb0kl0gjfb5c0vrjmwkfqvdf")))) + "1cys6frmbizc8bf933mwvvnr31sfya9ahcc0wm66pbd1x3mygkmk")))) (build-system r-build-system) (propagated-inputs `(("r-biobase" ,r-biobase) @@ -9735,14 +9743,14 @@ microarrays or GRanges for sequencing data.") (define-public r-keggrest (package (name "r-keggrest") - (version "1.24.1") + (version "1.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "KEGGREST" version)) (sha256 (base32 - "0yxp3iajdy61q6mjgp1nxdgmf2yb58cvqmdgab7lqxr0ky1wkfkr")))) + "1cgjvv9n88y3ah21356mh8z2l08vjn42hjy8hcljsibknzc4v247")))) (properties `((upstream-name . "KEGGREST"))) (build-system r-build-system) (propagated-inputs @@ -9759,14 +9767,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.34.0") + (version "2.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "08d5yg7n4rx4xsginc8bx0sycpj06pi1k7i44ff757444p20srwq")))) + "1qxfmg0id19iy3ia8h5nrvk3d1azqb28kl7m08i23654wb6b45c6")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9788,14 +9796,14 @@ analysis using other methods.") (define-public r-genomicfiles (package (name "r-genomicfiles") - (version "1.20.0") + (version "1.22.0") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFiles" version)) (sha256 (base32 - "122g0yhpsm6fyvv38agp57clagl13h324rk06mlgb2xz104a1j4i")))) + "1x6q827ms2l5lwzha1vsgfrshh35n9f19jq57xagrqlafxgpz86s")))) (properties `((upstream-name . "GenomicFiles"))) (build-system r-build-system) (propagated-inputs @@ -9821,14 +9829,14 @@ provide added flexibility for data combination and manipulation.") (define-public r-complexheatmap (package (name "r-complexheatmap") - (version "2.0.0") + (version "2.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ComplexHeatmap" version)) (sha256 (base32 - "1imnb72r10csl2h12sckic7hcsb8v2z0y3dyw1ax2fpykmsmq776")))) + "1pj6a6rmqckk033pkklk6hr4066rzavamy6w194rfdhind90rk0p")))) (properties `((upstream-name . "ComplexHeatmap"))) (build-system r-build-system) @@ -9853,14 +9861,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "0qirvhnbv4wd50ln4pqbk4dj6h2935ipf9p4sw1x62qqhwxidqk4")))) + "0knmncmkkf2ypyqfcl5s8nmyyf9nrzkqprzn9w3w8182c0v49r0s")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -9882,14 +9890,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.8.1") + (version "2.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "103z902104ljdp6s9y2dmgrl5wkdz8vvlbbqgk8r4drkg7m3d4lj")))) + "02lnpyp85zchmz404hr5381zmihvq4x9zgxdrbn2afi352vg0vab")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -9925,14 +9933,14 @@ chromosome region or transcript models of lincRNA genes.") (define-public r-organismdbi (package (name "r-organismdbi") - (version "1.26.0") + (version "1.28.0") (source (origin (method url-fetch) (uri (bioconductor-uri "OrganismDbi" version)) (sha256 (base32 - "14azk69pmwlhza0mhsxigsg127w3mgsx9hhrbdcdqmy3vzfbfaqq")))) + "1bvfyh733mhka9zd00hrzpalgjs255c2blnxyf60ipzk5jg7yllb")))) (properties `((upstream-name . "OrganismDbi"))) (build-system r-build-system) (propagated-inputs @@ -9957,14 +9965,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.32.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "1lba1801ak0a4vz6f8jffp9d525q27p0dhi2bp4f68mvdwwl2994")))) + "04vvj907bgs67w8rb7n1haf80p6cd0qj5fdxw0dwryb455y35vir")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -9999,14 +10007,14 @@ effort and encourages consistency.") (define-public r-ggbio (package (name "r-ggbio") - (version "1.32.0") + (version "1.34.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ggbio" version)) (sha256 (base32 - "10s6hnffnrrsx3896adqdc5g55fzd5y6qhnp1mq0c641nw833rwd")))) + "13wzwh40anh8l53yp19bg4w5cpxykcaf228dc8cxvjndyib711qb")))) (build-system r-build-system) (arguments `(#:phases @@ -10086,14 +10094,14 @@ organisms via the @code{g:Profiler} toolkit.") (define-public r-gqtlbase (package (name "r-gqtlbase") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLBase" version)) (sha256 (base32 - "1n2cizb88g2ankngvhxv377gizg80y3fhlx67sgm0z4ilm6a30ql")))) + "1qr8dqjbmj1mdjbzbnxwzfrm8f02wqfsgic8ws5kv7pmsby63y4x")))) (properties `((upstream-name . "gQTLBase"))) (build-system r-build-system) (propagated-inputs @@ -10121,14 +10129,14 @@ and more.") (define-public r-snpstats (package (name "r-snpstats") - (version "1.34.0") + (version "1.36.0") (source (origin (method url-fetch) (uri (bioconductor-uri "snpStats" version)) (sha256 (base32 - "0drfd24a5pkrhzmpidlh717bgh2dm68mpn6vj1vlpkilfbkifl34")))) + "1xq1rjljg70h5mshdza56dis0iv1a20sivs6dav3w5jbdd1l5qkh")))) (properties `((upstream-name . "snpStats"))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -10180,14 +10188,14 @@ several related annotation packages.") (define-public r-erma (package (name "r-erma") - (version "1.0.0") + (version "1.2.0") (source (origin (method url-fetch) (uri (bioconductor-uri "erma" version)) (sha256 (base32 - "0j7ggp63m5y88cxgi49vcql1s1avzifwvvd2hydj4lj3yrmzib48")))) + "085qsr73p8nyp435f15l4l1jkfd64bfd9gl4z496nfxdnqn95srz")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10218,14 +10226,14 @@ by Ernst and Kellis.") (define-public r-ldblock (package (name "r-ldblock") - (version "1.14.3") + (version "1.16.0") (source (origin (method url-fetch) (uri (bioconductor-uri "ldblock" version)) (sha256 (base32 - "154yvrvs8ik7ifcny1681cmqra0i163j00k4vbvkvl701p5gsp5q")))) + "0xpigfidmylfawy6vzshqnsw1lzjs4qms8q7zffij6bkvkv7920x")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) @@ -10233,8 +10241,6 @@ by Ernst and Kellis.") ("r-ensembldb" ,r-ensembldb) ("r-genomeinfodb" ,r-genomeinfodb) ("r-genomicfiles" ,r-genomicfiles) - ("r-go-db" ,r-go-db) - ("r-homo-sapiens" ,r-homo-sapiens) ("r-httr" ,r-httr) ("r-matrix" ,r-matrix) ("r-rsamtools" ,r-rsamtools) @@ -10252,14 +10258,14 @@ defining LD blocks.") (define-public r-gqtlstats (package (name "r-gqtlstats") - (version "1.16.0") + (version "1.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gQTLstats" version)) (sha256 (base32 - "17xadfn8qh1pwzlpcbds5wrjr9bzhsnmv90wffxmp02hq20qkrh5")))) + "1dly4p9r4231hf31xg1nzqiyvjbcfjljfmhb88ic1jxwnvniyv2f")))) (properties `((upstream-name . "gQTLstats"))) (build-system r-build-system) (propagated-inputs @@ -10306,14 +10312,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.28.3") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "0347r1ly0vzpilflzbyzsjdf4cday294lw3fxzx61clblrmws1ki")))) + "1p7n4yc77272rd8ybsim3rcg6kf6wmc95pwwav40b754imxn263z")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10352,14 +10358,14 @@ with your data.") (define-public r-gwascat (package (name "r-gwascat") - (version "2.16.1") + (version "2.18.0") (source (origin (method url-fetch) (uri (bioconductor-uri "gwascat" version)) (sha256 (base32 - "0d4krqx8zjniwp6k2vzwqgfws39w03x51kqiwd5dks1fp05sw4xh")))) + "038vhfsk2vs7inn5di093cmjbb81k7j0af385sg7l01jj70bdqq1")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10383,13 +10389,13 @@ EMBL-EBI GWAS catalog.") (define-public r-sushi (package (name "r-sushi") - (version "1.22.0") + (version "1.24.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Sushi" version)) (sha256 (base32 - "1hgh3jfcx0bh3fyvp85v7435hvsk3ah1hxx5117ss93v03iwjf1g")))) + "15xng21hd09fb234ravrry3b872zg82w8x9lijxab9n96xihcpz5")))) (properties `((upstream-name . "Sushi"))) (build-system r-build-system) (propagated-inputs @@ -10405,13 +10411,13 @@ visualizations for publication-quality multi-panel figures.") (define-public r-fithic (package (name "r-fithic") - (version "1.10.0") + (version "1.12.0") (source (origin (method url-fetch) (uri (bioconductor-uri "FitHiC" version)) (sha256 (base32 - "1qrxy4v8vmykrk8y6g3bs5wh5xhbs6pxyydbxy3vnj2mjirnxr6d")))) + "1irwkwi4afdj395134k31mvx7c2vpdd0rv8zrblnldascdsb04kc")))) (properties `((upstream-name . "FitHiC"))) (build-system r-build-system) (propagated-inputs @@ -10429,13 +10435,13 @@ assays such as Hi-C.") (define-public r-hitc (package (name "r-hitc") - (version "1.28.0") + (version "1.30.0") (source (origin (method url-fetch) (uri (bioconductor-uri "HiTC" version)) (sha256 (base32 - "059a1xxv2kb0bb32flymg2s8ylhavnv3j8l4125rfidagcgxgzjq")))) + "0byahi0fz0dzjyklz8v9whax9ygg7gwb4pl1j3zbl6z8a9qx8pps")))) (properties `((upstream-name . "HiTC"))) (build-system r-build-system) (propagated-inputs @@ -10458,14 +10464,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.12.3") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1037j6f0yyw4cf6p051810qamxi1sji5w4d0fgq5lyzyl5d36fm6")))) + "04hd02zd5jix5p2zg10asmwjg1fynqgmclbhbmk7fb6arx5hm11f")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs @@ -10474,6 +10480,7 @@ provided.") `(("r-biocgenerics" ,r-biocgenerics) ("r-delayedarray" ,r-delayedarray) ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) ("r-rhdf5" ,r-rhdf5) ("r-rhdf5lib" ,r-rhdf5lib) ("r-s4vectors" ,r-s4vectors))) @@ -10487,14 +10494,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.6.3") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "0q68n5jm7w99paibj8vkxbdksbyrxilzwc9dkp3zf8zrdc5qfxzy")) + "17lhwnm9rqsvbqkvwp0m07vjrk63a4389p2y39zffv8fgznxqzd7")) (modules '((guix build utils))) (snippet '(begin @@ -10511,10 +10518,14 @@ block processing.") (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 -lz'") - "'%s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'") - (("'%s/libhdf5.a %s/libsz.a -lz'") - "'%s/libhdf5.a %s/libhdf5.a -lz'")) + (("'\"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") + "'\"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") + (("'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libsz.a\" -lz'") + "'\"%s/libhdf5_cpp.a\" \"%s/libhdf5.a\" \"%s/libhdf5.a\" -lz'") + (("'%s/libhdf5_hl.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_hl.a %s/libhdf5.a %s/libhdf5.a -lz'") + (("'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libsz.a -lz'") + "'%s/libhdf5_hl_cpp.a %s/libhdf5_hl.a %s/libhdf5_cpp.a %s/libhdf5.a %s/libhdf5.a -lz'")) (with-directory-excursion "src" (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source")) (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10)) @@ -10539,6 +10550,14 @@ block processing.") (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") + (("HDF5_HL_INCLUDE=.*") "HDF5_HL_INCLUDE=./hdf5/hl/src\n") + (("HDF5_HL_CXX_INCLUDE=.*") "HDF5_HL_CXX_INCLUDE=./hdf5/hl/c++/src\n") + (("HDF5_HL_LIB=.*") + (string-append "HDF5_HL_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl.a\n")) + (("HDF5_HL_CXX_LIB=.*") + (string-append "HDF5_HL_CXX_LIB=" + (assoc-ref inputs "hdf5") "/lib/libhdf5_hl_cpp.a\n")) ;; szip is non-free software (("cp \"\\$\\{SZIP_LIB\\}.*") "") (("PKG_LIBS =.*") "PKG_LIBS = -lz -lhdf5\n"))) @@ -10558,18 +10577,19 @@ packages.") (define-public r-beachmat (package (name "r-beachmat") - (version "2.0.0") + (version "2.2.1") (source (origin (method url-fetch) (uri (bioconductor-uri "beachmat" version)) (sha256 (base32 - "14cz19fw97s8mhm9r2n5li44vckx069k8nqsyy64c3lkfm4vy4zx")))) + "1bpnlw2kdy9yc2vq948k980r0j25ipb80llhvn0j3kxjiwyfgs3i")))) (build-system r-build-system) (propagated-inputs `(("r-biocgenerics" ,r-biocgenerics) - ("r-delayedarray" ,r-delayedarray))) + ("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix))) (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 @@ -10580,14 +10600,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.6.0") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "0m3yjnv1njb4gyzcjfk7a0lz2vgggp2wjz382gqrb0qhhwcgfkj5")))) + "11pqb3cigi9xbhxq2k3n7z23v1ibd03ws1lcrh5c5ffgb33nlyw5")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -10607,13 +10627,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.12.2") + (version "1.14.6") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "16a17161xlhh6qpna9qxph3anlc7ydgyrczmy4alfiw8si7pzmxa")))) + "0sxd1s8wdlj9926bagq4crjrk1nnmh3j3bhgrw160zfgc3y8pzck")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10623,7 +10643,6 @@ libraries.") ("r-biocsingular" ,r-biocsingular) ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) - ("r-dplyr" ,r-dplyr) ("r-ggbeeswarm" ,r-ggbeeswarm) ("r-ggplot2" ,r-ggplot2) ("r-matrix" ,r-matrix) @@ -10642,14 +10661,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.12.1") + (version "1.14.5") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "17mknpkvs7mgnlbf2hv9k7rwbx2vlg60yrwfyb8nn3nxsb6vm7yn")))) + "0ydy6gvpgpvrs4ryk1qvmmxp6cpaizs294jwg42jawxndkds1l3y")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -10661,7 +10680,6 @@ quality control.") ("r-delayedarray" ,r-delayedarray) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dqrng" ,r-dqrng) - ("r-dynamictreecut" ,r-dynamictreecut) ("r-edger" ,r-edger) ("r-igraph" ,r-igraph) ("r-limma" ,r-limma) @@ -10683,14 +10701,14 @@ variable and significantly correlated genes.") (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") - (version "1.6.1") + (version "1.8.0") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedMatrixStats" version)) (sha256 (base32 - "1riyzfsq4bd513hidkw3cfkx3jywk3x87j89q70v459xsdfdc95b")))) + "0mv2rl6a6l404piabcazxz1s6ars016pxhjf5v40hhr6y1r0wbqy")))) (properties `((upstream-name . "DelayedMatrixStats"))) (build-system r-build-system) @@ -13272,21 +13290,23 @@ million cells.") (define-public python-bbknn (package (name "python-bbknn") - (version "1.3.1") + (version "1.3.6") (source (origin (method url-fetch) (uri (pypi-uri "bbknn" version)) (sha256 (base32 - "1qgdganvj3lyxj84v7alm23b9vqhwpn8z0115qndpnpy90qxynwz")))) + "1jbsh01f57zj4bhvjr3jh4532zznqd6nccmgrl3qi9gnhkf7c4y0")))) (build-system python-build-system) + (arguments + `(#:tests? #f)) ; TODO: Enable after migration to scikit-learn. (propagated-inputs `(("python-annoy" ,python-annoy) ("python-cython" ,python-cython) - ("python-faiss" ,python-faiss) ("python-numpy" ,python-numpy) - ("python-scanpy" ,python-scanpy))) + ("python-scipy" ,python-scipy) + ("python-umap-learn" ,python-umap-learn))) (home-page "https://github.com/Teichlab/bbknn") (synopsis "Batch balanced KNN") (description "BBKNN is a batch effect removal tool that can be directly @@ -13419,14 +13439,14 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.5.4.2") + (version "0.5.7") (source (origin (method url-fetch) (uri (pypi-uri "pyfaidx" version)) (sha256 (base32 - "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) + "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six))) @@ -15370,3 +15390,92 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public python-gffutils + ;; The latest release is older more than a year than the latest commit + (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") + (revision "1")) + (package + (name "python-gffutils") + (version (git-version "0.9" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Tests need to access the HOME directory + (setenv "HOME" "/tmp") + (invoke "nosetests" "-a" "!slow"))) + (add-after 'unpack 'make-gz-files-writable + (lambda _ + (for-each make-file-writable + (find-files "." "\\.gz")) + #t))))) + (propagated-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-argh" ,python-argh) + ("python-biopython" ,python-biopython) + ("python-pybedtools" ,python-pybedtools) + ("python-pyfaidx" ,python-pyfaidx) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) + (native-inputs + `(("python-nose" , python-nose))) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating +the GFF and GTF format files typically used for genomic annotations. The +files are loaded into a SQLite database, allowing much more complex +manipulation of hierarchical features (e.g., genes, transcripts, and exons) +than is possible with plain-text methods alone.") + (license license:expat)))) + +(define-public libsbml + (package + (name "libsbml") + (version "5.18.0") + (source (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/sbml/libsbml/" + version "/stable/libSBML-" + version "-core-src.tar.gz")) + (sha256 + (base32 + "0slkagrk3nfi2qsksv6b1brj6zhx4bj4bkib2sdycvrcd10ql2lh")))) + (build-system cmake-build-system) + (arguments + `(#:test-target "test" + #:configure-flags + (list "-DWITH_CHECK=ON" + (string-append "-DLIBXML_LIBRARY=" + (assoc-ref %build-inputs "libxml2") + "/lib/libxml2.so") + (string-append "-DLIBXML_INCLUDE_DIR=" + (assoc-ref %build-inputs "libxml2") + "/include/libxml2")))) + (propagated-inputs + `(("libxml2" ,libxml2))) + (native-inputs + `(("check" ,check) + ("swig" ,swig))) + (home-page "http://sbml.org/Software/libSBML") + (synopsis "Process SBML files and data streams") + (description "LibSBML is a library to help you read, write, manipulate, +translate, and validate SBML files and data streams. The @dfn{Systems Biology +Markup Language} (SBML) is an interchange format for computer models of +biological processes. SBML is useful for models of metabolism, cell +signaling, and more. It continues to be evolved and expanded by an +international community.") + (license license:lgpl2.1+))) |