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-rw-r--r--gnu/packages/bioinformatics.scm315
1 files changed, 143 insertions, 172 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5105bfab4f..23eba74175 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1,10 +1,10 @@
;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014, 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2015 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com>
;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
@@ -72,12 +72,14 @@
#:use-module (gnu packages graph)
#:use-module (gnu packages groff)
#:use-module (gnu packages guile)
+ #:use-module (gnu packages guile-xyz)
#:use-module (gnu packages haskell)
#:use-module (gnu packages haskell-check)
#:use-module (gnu packages haskell-web)
#: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)
@@ -97,7 +99,9 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
+ #:use-module (gnu packages python-compression)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages serialization)
@@ -2298,6 +2302,22 @@ data and settings.")
("cairo" ,cairo)))
(native-inputs
`(("texlive" ,texlive)
+ ;; TODO: Replace texlive with minimal texlive-union.
+ ;; ("texlive" ,(texlive-union (list texlive-latex-doi
+ ;; texlive-latex-hyperref
+ ;; texlive-latex-oberdiek
+ ;; texlive-generic-ifxetex
+ ;; texlive-latex-url
+ ;; texlive-latex-pgf
+ ;; texlive-latex-examplep
+ ;; texlive-latex-natbib
+ ;; texlive-latex-verbatimbox
+ ;; texlive-latex-ms
+ ;; texlive-latex-xcolor
+ ;; texlive-fonts-amsfonts
+ ;; texlive-latex-amsfonts
+ ;; ;; ...
+ ;; )))
("imagemagick" ,imagemagick)))
(home-page "http://dorina.mdc-berlin.de/public/rajewsky/discrover/")
(synopsis "Discover discriminative nucleotide sequence motifs")
@@ -4484,9 +4504,7 @@ files and writing bioinformatics applications.")
(source
(origin
(method url-fetch)
- (uri (string-append
- "https://pypi.python.org/packages/source/W/WarpedLMM/WarpedLMM-"
- version ".zip"))
+ (uri (pypi-uri "WarpedLMM" version ".zip"))
(sha256
(base32
"1agfz6zqa8nc6cw47yh0s3y14gkpa9wqazwcj7mwwj3ffnw39p3j"))))
@@ -6002,7 +6020,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(define-public star
(package
(name "star")
- (version "2.6.0c")
+ (version "2.7.0a")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -6011,7 +6029,7 @@ application of SortMeRNA is filtering rRNA from metatranscriptomic data.")
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
- "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59"))
+ "1yx28gra6gqdx1ps5y8mpdinsn8r0dhsc2m3gcvjfrk71i9yhd6l"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -6321,63 +6339,6 @@ between two different types of motif instances using as much relevant
information as possible.")
(license (list license:gpl2+ license:gpl3+))))
-(define-public r-vegan
- (package
- (name "r-vegan")
- (version "2.5-3")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "vegan" version))
- (sha256
- (base32
- "023xznh0iy0496icpchadmp7a3rk3nj9s48fvwlvp3dssw58yp3c"))))
- (build-system r-build-system)
- (native-inputs
- `(("gfortran" ,gfortran)))
- (propagated-inputs
- `(("r-cluster" ,r-cluster)
- ("r-knitr" ,r-knitr) ; needed for vignettes
- ("r-lattice" ,r-lattice)
- ("r-mass" ,r-mass)
- ("r-mgcv" ,r-mgcv)
- ("r-permute" ,r-permute)))
- (home-page "https://cran.r-project.org/web/packages/vegan")
- (synopsis "Functions for community ecology")
- (description
- "The vegan package provides tools for descriptive community ecology. It
-has most basic functions of diversity analysis, community ordination and
-dissimilarity analysis. Most of its multivariate tools can be used for other
-data types as well.")
- (license license:gpl2+)))
-
-(define-public r-annotate
- (package
- (name "r-annotate")
- (version "1.60.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "annotate" version))
- (sha256
- (base32
- "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-annotationdbi" ,r-annotationdbi)
- ("r-biobase" ,r-biobase)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-dbi" ,r-dbi)
- ("r-rcurl" ,r-rcurl)
- ("r-xml" ,r-xml)
- ("r-xtable" ,r-xtable)))
- (home-page
- "https://bioconductor.org/packages/annotate")
- (synopsis "Annotation for microarrays")
- (description "This package provides R environments for the annotation of
-microarrays.")
- (license license:artistic2.0)))
-
(define-public r-copynumber
(package
(name "r-copynumber")
@@ -6456,14 +6417,14 @@ 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
@@ -6493,14 +6454,14 @@ 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
@@ -6566,14 +6527,14 @@ 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)))
@@ -6718,14 +6679,14 @@ 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
@@ -7075,26 +7036,6 @@ use multiple corrections. Visualization of data can be done either by
barplots or heatmaps.")
(license license:gpl2+)))
-(define-public r-biocgenerics
- (package
- (name "r-biocgenerics")
- (version "0.28.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "BiocGenerics" version))
- (sha256
- (base32
- "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
- (properties
- `((upstream-name . "BiocGenerics")))
- (build-system r-build-system)
- (home-page "https://bioconductor.org/packages/BiocGenerics")
- (synopsis "S4 generic functions for Bioconductor")
- (description
- "This package provides S4 generic functions needed by many Bioconductor
-packages.")
- (license license:artistic2.0)))
-
(define-public r-biocinstaller
(package
(name "r-biocinstaller")
@@ -7117,13 +7058,13 @@ 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)
@@ -7144,13 +7085,13 @@ 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)
@@ -7241,14 +7182,14 @@ checks on R packages that are to be submitted to the Bioconductor repository.")
(define-public r-optparse
(package
(name "r-optparse")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "optparse" version))
(sha256
(base32
- "1d7v5gl45x4amsfmzn5zyyffyqlc7a82h01szlnda22viyxids0h"))))
+ "04vyb6dhcga30mvghsg1p052jmf69xqxkvh3hzqz7dscyppy76w1"))))
(build-system r-build-system)
(propagated-inputs
`(("r-getopt" ,r-getopt)))
@@ -7418,13 +7359,13 @@ 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
@@ -7446,13 +7387,13 @@ CAGE.")
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.28.1")
+ (version "1.28.10")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "0gvah258mkaafhbna81zwknx8qr3lidbcx5qvwk39q3yswr9mi49"))))
+ "0kxf583cgkdz1shi85r0mpnfxmzi7s5f6srd1czbdl2iibvrm8jn"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
@@ -7484,13 +7425,13 @@ 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")
@@ -7650,13 +7591,13 @@ 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)
@@ -7675,13 +7616,13 @@ 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)
@@ -7807,13 +7748,13 @@ 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)
@@ -7840,13 +7781,13 @@ 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
@@ -7887,13 +7828,13 @@ as well as query and modify the browser state, such as the current viewport.")
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.34.1")
+ (version "1.34.2")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6"))))
+ "0qs94b0ywrjyc9m1jykrbch3lb07576m508dikvx18vwn304mban"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
@@ -8544,7 +8485,7 @@ throughput genetic sequencing data sets using regression methods.")
(define-public r-qtl
(package
(name "r-qtl")
- (version "1.42-8")
+ (version "1.44-9")
(source
(origin
(method url-fetch)
@@ -8552,7 +8493,7 @@ throughput genetic sequencing data sets using regression methods.")
version ".tar.gz"))
(sha256
(base32
- "1l528dwvfpdlr05imrrm4rq32axp6hld9nqm6mm43kn5n7z2f5k6"))))
+ "03lmvydln8b7666b6w46qbryhf83vsd11d4y2v95rfgvqgq66l1i"))))
(build-system r-build-system)
(home-page "http://rqtl.org/")
(synopsis "R package for analyzing QTL experiments in genetics")
@@ -8937,13 +8878,13 @@ 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")
@@ -8959,13 +8900,13 @@ 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)))
@@ -9189,8 +9130,7 @@ may optionally be provided to further inform the peak-calling process.")
(version "1.0.9")
(source (origin
(method url-fetch)
- (uri (string-append "https://pypi.python.org/packages/source/P"
- "/PePr/PePr-" version ".tar.gz"))
+ (uri (pypi-uri "PePr" version))
(sha256
(base32
"0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
@@ -9344,14 +9284,14 @@ 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
@@ -9384,13 +9324,13 @@ 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
@@ -9430,14 +9370,14 @@ 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)
@@ -9460,14 +9400,14 @@ 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)))
@@ -9560,14 +9500,14 @@ 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
@@ -9698,14 +9638,14 @@ 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
@@ -9758,14 +9698,14 @@ 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
@@ -9801,14 +9741,14 @@ 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
@@ -9930,14 +9870,14 @@ 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
@@ -9961,14 +9901,14 @@ 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
@@ -9976,6 +9916,7 @@ 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)
@@ -10023,14 +9964,14 @@ 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
@@ -10112,14 +10053,14 @@ 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)
@@ -10204,14 +10145,14 @@ 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)
@@ -10233,14 +10174,14 @@ 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)
@@ -10308,14 +10249,14 @@ 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
@@ -10645,14 +10586,14 @@ 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
@@ -10806,14 +10747,14 @@ 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)
@@ -10835,14 +10776,14 @@ 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
@@ -10861,14 +10802,14 @@ 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
@@ -10961,14 +10902,14 @@ 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)
@@ -10988,13 +10929,13 @@ 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)
@@ -11024,14 +10965,14 @@ 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)
@@ -13269,6 +13210,41 @@ descriptive settings file. The result is a set of comprehensive, interactive
HTML reports with interesting findings about your samples.")
(license license:gpl3+)))
+(define-public mantis
+ (let ((commit "4ffd171632c2cb0056a86d709dfd2bf21bc69b84")
+ (revision "1"))
+ (package
+ (name "mantis")
+ (version (git-version "0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/splatlab/mantis.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0iqbr0dhmlc8mzpirmm2s4pkzkwdgrcx50yx6cv3wlr2qi064p55"))))
+ (build-system cmake-build-system)
+ (arguments '(#:tests? #f)) ; there are none
+ (inputs
+ `(("sdsl-lite" ,sdsl-lite)
+ ("openssl" ,openssl)
+ ("zlib" ,zlib)))
+ (home-page "https://github.com/splatlab/mantis")
+ (synopsis "Large-scale sequence-search index data structure")
+ (description "Mantis is a space-efficient data structure that can be
+used to index thousands of raw-read genomics experiments and facilitate
+large-scale sequence searches on those experiments. Mantis uses counting
+quotient filters instead of Bloom filters, enabling rapid index builds and
+queries, small indexes, and exact results, i.e., no false positives or
+negatives. Furthermore, Mantis is also a colored de Bruijn graph
+representation, so it supports fast graph traversal and other topological
+analyses in addition to large-scale sequence-level searches.")
+ ;; uses __uint128_t and inline assembly
+ (supported-systems '("x86_64-linux"))
+ (license license:bsd-3))))
+
(define-public r-diversitree
(package
(name "r-diversitree")
@@ -14166,12 +14142,7 @@ 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"))
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-09 11:16:32 +0000