diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 157 |
1 files changed, 77 insertions, 80 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 58ba2f05d6..42f5c3b80d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -78,6 +78,7 @@ #:use-module (gnu packages image) #:use-module (gnu packages imagemagick) #:use-module (gnu packages java) + #:use-module (gnu packages java-compression) #:use-module (gnu packages jemalloc) #:use-module (gnu packages dlang) #:use-module (gnu packages linux) @@ -6472,14 +6473,14 @@ high-throughput sequencing experiments.") (define-public r-deseq2 (package (name "r-deseq2") - (version "1.22.1") + (version "1.22.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq2" version)) (sha256 (base32 - "1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5")))) + "0n5ah84mxn87p45drzy0wh2yknmzj1q5i6gv0v9vgg1lj7awb91r")))) (properties `((upstream-name . "DESeq2"))) (build-system r-build-system) (propagated-inputs @@ -6509,14 +6510,14 @@ distribution.") (define-public r-dexseq (package (name "r-dexseq") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DEXSeq" version)) (sha256 (base32 - "0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8")))) + "0g5w9bn2nb3m670hkcsnhfvvkza2318z9irlhhwhb3n8rdzlsdym")))) (properties `((upstream-name . "DEXSeq"))) (build-system r-build-system) (propagated-inputs @@ -6582,14 +6583,14 @@ databases. Packages produced are intended to be used with AnnotationDbi.") (define-public r-rbgl (package (name "r-rbgl") - (version "1.58.0") + (version "1.58.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RBGL" version)) (sha256 (base32 - "0jy95m38c4qp0a12097hhm2gg63k96k6ydhb11dy379h3ziapcar")))) + "1l5x2icv9di1lr3gqfi0vjnyd9xc3l77yc42ippqd4cadj3d1pzf")))) (properties `((upstream-name . "RBGL"))) (build-system r-build-system) (propagated-inputs `(("r-graph" ,r-graph))) @@ -6734,14 +6735,14 @@ ungapped alignment formats.") (define-public r-systempiper (package (name "r-systempiper") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "systemPipeR" version)) (sha256 (base32 - "0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04")))) + "0qzydz87rld2nhwzbfgrw5jfgh8maa9y54mjx9c4285m11qj2shq")))) (properties `((upstream-name . "systemPipeR"))) (build-system r-build-system) (propagated-inputs @@ -7133,13 +7134,13 @@ Bioconductor, CRAN, and Github.") (define-public r-biocviews (package (name "r-biocviews") - (version "1.50.5") + (version "1.50.10") (source (origin (method url-fetch) (uri (bioconductor-uri "biocViews" version)) (sha256 (base32 - "0rc1n89n04ylvy9gvsgvizcs77bh70jg1nkjjsjs7rqbr3zzdysz")))) + "06ms82pyc5rxbd9crfvqjxcwpafv0c627i83v80d12925mrc51h8")))) (properties `((upstream-name . "biocViews"))) (build-system r-build-system) @@ -7160,13 +7161,13 @@ also known as views, in a controlled vocabulary.") (define-public r-bookdown (package (name "r-bookdown") - (version "0.7") + (version "0.9") (source (origin (method url-fetch) (uri (cran-uri "bookdown" version)) (sha256 (base32 - "1b3fw1f41zph5yw3kynb47aijq53vhaa6mnnvxly72zamyzdf95q")))) + "0vg1s1w0l9pm95asqb21yf39mfk1nc9rdhmlys9xwr7p7i7rsz32")))) (build-system r-build-system) (propagated-inputs `(("r-htmltools" ,r-htmltools) @@ -7434,13 +7435,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.24.0") + (version "3.24.3") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0ihihgzrgb4q3xc8xkzp1v76ndgihrj4gas00fa25vggfs1v6hvg")))) + "15yimsbsxmxhlsfmgw5j7fd8qn08zz4xqxrir1c6n2dc103y22xg")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs @@ -7462,13 +7463,13 @@ CAGE.") (define-public r-variantannotation (package (name "r-variantannotation") - (version "1.28.1") + (version "1.28.8") (source (origin (method url-fetch) (uri (bioconductor-uri "VariantAnnotation" version)) (sha256 (base32 - "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49")))) + "0gf36lr9xy3zmcc4rxs5bi2ccrrc7b6wqp6p3cvnclgif4i0l66k")))) (properties `((upstream-name . "VariantAnnotation"))) (inputs @@ -7500,13 +7501,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.38.2") + (version "3.38.3") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1wkh362rmn24q7bkinb6nx62a31wl3r3myg5l326gx65wpwdnx97")))) + "08va8jggmv61wym955mnb1n31mgikrmjys7dl1kp5hp3yia8jg7l")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") @@ -7666,13 +7667,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.16.0") + (version "1.16.5") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0g16cy0vjapqkb188z63r1b6y96m9g8vx0a3v2qavzxc177k0cja")))) + "1164dk0fajb2vrkfpcjs11055qf1cs4vvbnq0aqdaaf2p4lyx41l")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) @@ -7691,13 +7692,13 @@ objects.") (define-public r-biostrings (package (name "r-biostrings") - (version "2.50.1") + (version "2.50.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Biostrings" version)) (sha256 (base32 - "1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8")))) + "16cqqc8i6gb0jcz0lizfqqxsq7g0yb0ll2s9qzmb45brp07dg8f7")))) (properties `((upstream-name . "Biostrings"))) (build-system r-build-system) @@ -7823,13 +7824,13 @@ samples.") (define-public r-genomicalignments (package (name "r-genomicalignments") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicAlignments" version)) (sha256 (base32 - "0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24")))) + "1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd")))) (properties `((upstream-name . "GenomicAlignments"))) (build-system r-build-system) @@ -7856,13 +7857,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.42.0") + (version "1.42.1") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "0a4mhd926w9slkfil5xgngjsfdj024a4w57w2bm3d4r0pj8y5da7")))) + "1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6")))) (build-system r-build-system) (arguments `(#:phases @@ -8953,13 +8954,13 @@ kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") (define-public r-tximport (package (name "r-tximport") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "tximport" version)) (sha256 (base32 - "0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h")))) + "16wp09dm0cpb4mc00nmglfb8ica7qb4a55vm8ajgzyagbpfdd44l")))) (build-system r-build-system) (home-page "https://bioconductor.org/packages/tximport") (synopsis "Import and summarize transcript-level estimates for gene-level analysis") @@ -8975,13 +8976,13 @@ of gene-level counts.") (define-public r-rhdf5 (package (name "r-rhdf5") - (version "2.26.0") + (version "2.26.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rhdf5" version)) (sha256 (base32 - "0xmpkfdsmgl79ffffj7cf9fx3zxki2rk0xn25k778kr3s0sbmhis")))) + "10zkw3k13wmvyif417gplyf6rwp2gpkjasw97lhwv2f9i32rry9l")))) (build-system r-build-system) (propagated-inputs `(("r-rhdf5lib" ,r-rhdf5lib))) @@ -9360,14 +9361,14 @@ GenomicRanges Bioconductor package.") (define-public r-copywriter (package (name "r-copywriter") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "CopywriteR" version)) (sha256 (base32 - "0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn")))) + "1hbiw0m9hmx4na9v502pxf8y5wvxzr68r4d3fqr2755gxx86qck6")))) (properties `((upstream-name . "CopywriteR"))) (build-system r-build-system) (propagated-inputs @@ -9400,13 +9401,13 @@ number detection tools.") (define-public r-methylkit (package (name "r-methylkit") - (version "1.8.0") + (version "1.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "methylKit" version)) (sha256 (base32 - "0mz6lil1wax931incnw5byx0v9i8ryhwq9mv0nv8s48ai33ch3x6")))) + "1zcfwy7i10aqgnf7r0c41hakb5aai3s3n9y8pc6a98vimz51ly2z")))) (properties `((upstream-name . "methylKit"))) (build-system r-build-system) (propagated-inputs @@ -9446,14 +9447,14 @@ TAB-Seq.") (define-public r-sva (package (name "r-sva") - (version "3.30.0") + (version "3.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "sva" version)) (sha256 (base32 - "1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3")))) + "0czja4c5jxa0g3fspi90nyajqmvzb29my4ykv2wi66h43f5dlwhq")))) (build-system r-build-system) (propagated-inputs `(("r-genefilter" ,r-genefilter) @@ -9476,14 +9477,14 @@ unmodeled, or latent sources of noise.") (define-public r-seqminer (package (name "r-seqminer") - (version "6.1") + (version "7.1") (source (origin (method url-fetch) (uri (cran-uri "seqminer" version)) (sha256 (base32 - "15yhg4vfc7jg1jnqb3371j00pgbmbyc9l1xx63hq1l3p34lazq2l")))) + "1jydcpkw4rwfp983j83kipvsvr10as9pb49zzn3c2v09k1gh3ymy")))) (build-system r-build-system) (inputs `(("zlib" ,zlib))) @@ -9576,14 +9577,14 @@ proteomics packages.") (define-public r-mzr (package (name "r-mzr") - (version "2.16.0") + (version "2.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzR" version)) (sha256 (base32 - "0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5")) + "0mlwg646k49klxrznckzfv54a9mz6irj42fqpaaa0xjm6cw2lwaa")) (modules '((guix build utils))) (snippet '(begin @@ -9714,14 +9715,14 @@ and specific in detecting differential transcription.") (define-public r-mzid (package (name "r-mzid") - (version "1.20.0") + (version "1.20.1") (source (origin (method url-fetch) (uri (bioconductor-uri "mzID" version)) (sha256 (base32 - "08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz")))) + "15yd4bdxprw3kg7zj2k652y3yr3si781iw28jqvnkm0gsc23rd0c")))) (properties `((upstream-name . "mzID"))) (build-system r-build-system) (propagated-inputs @@ -9774,14 +9775,14 @@ structure (pcaRes) to provide a common interface to the PCA results.") (define-public r-msnbase (package (name "r-msnbase") - (version "2.8.1") + (version "2.8.3") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnbase" version)) (sha256 (base32 - "0y658anh06vnvbkfs7r8q40gqgyqr2r8kj7jlpnp33fy1lvp1nv7")))) + "1kl1d7byphnfpmbl5fzbgs68dxskhpsdyx7ka51bpfn0nv3pp492")))) (properties `((upstream-name . "MSnbase"))) (build-system r-build-system) (propagated-inputs @@ -9817,14 +9818,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.16.0") + (version "1.16.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "0hgq4argllhh5hvxqi8vkf1blc3nibsslhx4zsv2mcv4yj75bv4n")))) + "077n6ljcnnl7q4w0qj8v46vm4sjk9vzzfqf7wsc6lz0wmyzqdng3")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs @@ -9946,14 +9947,14 @@ classes.") (define-public r-deseq (package (name "r-deseq") - (version "1.34.0") + (version "1.34.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DESeq" version)) (sha256 (base32 - "1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya")))) + "0bpiixczbhlyaiinpbl6xrpmv72k2bq76bxnw06gl35m4pgs94p2")))) (properties `((upstream-name . "DESeq"))) (build-system r-build-system) (propagated-inputs @@ -9977,14 +9978,14 @@ distribution.") (define-public r-edaseq (package (name "r-edaseq") - (version "2.16.0") + (version "2.16.3") (source (origin (method url-fetch) (uri (bioconductor-uri "EDASeq" version)) (sha256 (base32 - "1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf")))) + "0559ph606ps2g9bwbl0a2knkcs5w581n9igngpjxvk5p56k24gb5")))) (properties `((upstream-name . "EDASeq"))) (build-system r-build-system) (propagated-inputs @@ -9992,6 +9993,7 @@ distribution.") ("r-aroma-light" ,r-aroma-light) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) + ("r-biocmanager" ,r-biocmanager) ("r-biomart" ,r-biomart) ("r-biostrings" ,r-biostrings) ("r-deseq" ,r-deseq) @@ -10039,14 +10041,14 @@ Shiny-based display methods for Bioconductor objects.") (define-public r-annotationhub (package (name "r-annotationhub") - (version "2.14.1") + (version "2.14.2") (source (origin (method url-fetch) (uri (bioconductor-uri "AnnotationHub" version)) (sha256 (base32 - "00288x3na0izpmbcvsqac1br1qwry86vwc2slj1l47crdfb7za6c")))) + "17fgrvcnbii9siv5rq5j09bxhqffx47f6jf10418qvr7hh61ic1g")))) (properties `((upstream-name . "AnnotationHub"))) (build-system r-build-system) (propagated-inputs @@ -10128,14 +10130,14 @@ microarrays or GRanges for sequencing data.") (define-public r-gage (package (name "r-gage") - (version "2.32.0") + (version "2.32.1") (source (origin (method url-fetch) (uri (bioconductor-uri "gage" version)) (sha256 (base32 - "07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931")))) + "02g796sb1800ff0f1mq9f2m5wwzpf8pnfzajs49i68dhq2hm01a8")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10220,14 +10222,14 @@ self-defined annotation graphics.") (define-public r-dirichletmultinomial (package (name "r-dirichletmultinomial") - (version "1.24.0") + (version "1.24.1") (source (origin (method url-fetch) (uri (bioconductor-uri "DirichletMultinomial" version)) (sha256 (base32 - "19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f")))) + "0vazfjzqy78p5g7dnv30lbqbj4bhq4zafd2wh6gdwy2il1fd78xa")))) (properties `((upstream-name . "DirichletMultinomial"))) (build-system r-build-system) @@ -10249,14 +10251,14 @@ originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): (define-public r-ensembldb (package (name "r-ensembldb") - (version "2.6.2") + (version "2.6.3") (source (origin (method url-fetch) (uri (bioconductor-uri "ensembldb" version)) (sha256 (base32 - "0hdz1f34v7sas2v4225icwl3wd4sf17ykpd5dkbx1hc7wcy4w3np")))) + "0kzdsfk6mdwlp57sw4j2cf7lx5nc67v5j0xr3iag9kzmgikaq1lb")))) (build-system r-build-system) (propagated-inputs `(("r-annotationdbi" ,r-annotationdbi) @@ -10324,14 +10326,14 @@ the fact that each of these packages implements a select methods.") (define-public r-biovizbase (package (name "r-biovizbase") - (version "1.30.0") + (version "1.30.1") (source (origin (method url-fetch) (uri (bioconductor-uri "biovizBase" version)) (sha256 (base32 - "0v54mcn3rnnfx8dmcrms5z3rgq19n3hp4r23azlgzwq6hjw7cccx")))) + "0v5gvcx180qn5487i1dph9abadw3ggqwp5yzy41jswzbdc8q6sbm")))) (properties `((upstream-name . "biovizBase"))) (build-system r-build-system) (propagated-inputs @@ -10661,14 +10663,14 @@ family of feature/genome hypotheses.") (define-public r-gviz (package (name "r-gviz") - (version "1.26.0") + (version "1.26.4") (source (origin (method url-fetch) (uri (bioconductor-uri "Gviz" version)) (sha256 (base32 - "05zk9hf30afg6rjg97lzn5v8xij90v8zm09y9vcz0asmc3c8xs0a")))) + "0jvcivgw0ahv2rjadxmrww76xambhf7silczmh38nn4yn4qw6w9y")))) (properties `((upstream-name . "Gviz"))) (build-system r-build-system) (propagated-inputs @@ -10822,14 +10824,14 @@ provided.") (define-public r-qvalue (package (name "r-qvalue") - (version "2.14.0") + (version "2.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "qvalue" version)) (sha256 (base32 - "03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a")))) + "0kxavzm1j2mk26qicmjm90nxx4w5h3dxighzks7wzihay3k8cysc")))) (build-system r-build-system) (propagated-inputs `(("r-ggplot2" ,r-ggplot2) @@ -10851,14 +10853,14 @@ problems in genomics, brain imaging, astrophysics, and data mining.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "1w7ad8cfsbh5xx82m3l4lc0vbmj9lcsqxxpiy3ana2ycgn1bqv3g")))) + "1qwdsygcadl58qj598hfyvs8hp0hqcl9ghnhknahrlhmb7k2bd2d")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (propagated-inputs @@ -10877,14 +10879,14 @@ block processing.") (define-public r-rhdf5lib (package (name "r-rhdf5lib") - (version "1.4.0") + (version "1.4.2") (source (origin (method url-fetch) (uri (bioconductor-uri "Rhdf5lib" version)) (sha256 (base32 - "01gpz780g850ql20b2ql6pvr678ydk4nq4sn5iiih94a4crb9lz1")) + "06bxd3wz8lrvh2hzvmjpdv4lvzj5lz9353bw5b3zb98cb8w9r2j5")) (modules '((guix build utils))) (snippet '(begin @@ -10977,14 +10979,14 @@ matrices.") (define-public r-singlecellexperiment (package (name "r-singlecellexperiment") - (version "1.4.0") + (version "1.4.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SingleCellExperiment" version)) (sha256 (base32 - "19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj")))) + "12139kk9cqgzpm6f3cwdsq31gj5lxamz2q939dy9fa0fa54gdaq4")))) (properties `((upstream-name . "SingleCellExperiment"))) (build-system r-build-system) @@ -11004,13 +11006,13 @@ libraries.") (define-public r-scater (package (name "r-scater") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "scater" version)) (sha256 (base32 - "1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3")))) + "0rijhy7g5qmcn927y1wyd63la1fhyar9fv1hccsqd23jd98yc55a")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -11040,14 +11042,14 @@ quality control.") (define-public r-scran (package (name "r-scran") - (version "1.10.1") + (version "1.10.2") (source (origin (method url-fetch) (uri (bioconductor-uri "scran" version)) (sha256 (base32 - "1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03")))) + "07mgilr3gq3lnrm1fjm9zhz4w7970bjhsykln1drqy9gkzj5sn7g")))) (build-system r-build-system) (propagated-inputs `(("r-beachmat" ,r-beachmat) @@ -14217,12 +14219,7 @@ absolute GSEA.") #:phases (modify-phases %standard-phases (delete 'configure) - (replace 'build - (lambda* (#:key inputs outputs #:allow-other-keys) - (substitute* "JAMM.sh" - (("^sPath=.*") - (string-append ""))) - #t)) + (delete 'build) (replace 'install (lambda* (#:key inputs outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) |