(define-public r-genefilter
(package
(name "r-genefilter")
- (version "1.64.0")
+ (version "1.66.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "genefilter" version))
(sha256
(base32
- "0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i"))))
+ "1jq7lam4dnbvz55lx93kcl9afl8xfjd6xs374d35m21bkay418kj"))))
(build-system r-build-system)
(native-inputs
`(("gfortran" ,gfortran)))
(define-public r-deseq2
(package
(name "r-deseq2")
- (version "1.22.2")
+ (version "1.24.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DESeq2" version))
(sha256
(base32
- "0n5ah84mxn87p45drzy0wh2yknmzj1q5i6gv0v9vgg1lj7awb91r"))))
+ "0fkk326addm2cw688gnmdzsmri5qx8j6ldnr4xin6kjnwicqhlqd"))))
(properties `((upstream-name . "DESeq2")))
(build-system r-build-system)
(propagated-inputs
(define-public r-dexseq
(package
(name "r-dexseq")
- (version "1.28.3")
+ (version "1.30.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DEXSeq" version))
(sha256
(base32
- "1wsj1kqfrakmjnlplxmrv17r2spzcdkmwdkhggyjbf8mdhqs3w16"))))
+ "1b2s0vwm97g0wgm4ms0f4pqkqiqmxscnhg700aybl5vx0m2fa8xm"))))
(properties `((upstream-name . "DEXSeq")))
(build-system r-build-system)
(propagated-inputs
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.24.0")
+ (version "1.26.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"))))
+ "0m4w8n2711wr28znv646cfc7m5jqlr8friz334zdyjmhg7m2xkb7"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
(define-public r-rbgl
(package
(name "r-rbgl")
- (version "1.58.2")
+ (version "1.60.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "RBGL" version))
(sha256
(base32
- "0vhnh47pswnp27c0zqcbnnsayfmq3cxcgrs9g860555ldqfl4cyl"))))
+ "06brn9hl6lybx6hdfp1sycwj6wn1bjfi8xyhpy0v122v1z8d5mbz"))))
(properties `((upstream-name . "RBGL")))
(build-system r-build-system)
- (propagated-inputs `(("r-graph" ,r-graph)))
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-graph" ,r-graph)))
(home-page "https://www.bioconductor.org/packages/RBGL")
(synopsis "Interface to the Boost graph library")
(description
(define-public r-gseabase
(package
(name "r-gseabase")
- (version "1.44.0")
+ (version "1.46.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GSEABase" version))
(sha256
(base32
- "110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr"))))
+ "0vh53xk2prjbdkbr3hwfiflx1gh7ilrqs3j1p3lyd6syy3rn9n83"))))
(properties `((upstream-name . "GSEABase")))
(build-system r-build-system)
(propagated-inputs
(define-public r-category
(package
(name "r-category")
- (version "2.48.1")
+ (version "2.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Category" version))
(sha256
(base32
- "18rsxlwa1l06i635cnznb9b2zssqcgb71pihky29gl2gwp7a654b"))))
+ "1n36xfnwn2np5f0lix9abvv9w6jb25jqz3xzvqzklz9s1af4k6x4"))))
(properties `((upstream-name . "Category")))
(build-system r-build-system)
(propagated-inputs
(define-public r-gostats
(package
(name "r-gostats")
- (version "2.48.0")
+ (version "2.50.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "GOstats" version))
(sha256
(base32
- "0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln"))))
+ "1a95i6awm2a8xv42fg2z3n29fg9z29i45kd80hxf6mvqqgzj80xp"))))
(properties `((upstream-name . "GOstats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-shortread
(package
(name "r-shortread")
- (version "1.40.0")
+ (version "1.42.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ShortRead" version))
(sha256
(base32
- "0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1"))))
+ "1irqzdgsavjqsq0vva4966qh8qgn7xn9382dmhahm1hxb94qmi59"))))
(properties `((upstream-name . "ShortRead")))
(build-system r-build-system)
(inputs
(define-public r-grohmm
(package
(name "r-grohmm")
- (version "1.16.0")
+ (version "1.18.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "groHMM" version))
(sha256
(base32
- "1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh"))))
+ "1p368qf8ab1vy8gl2j7rx0l7bvva4m7w06i364rqzs0sdyzlbm3y"))))
(properties `((upstream-name . "groHMM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.50.10")
+ (version "1.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "06ms82pyc5rxbd9crfvqjxcwpafv0c627i83v80d12925mrc51h8"))))
+ "1wc7a953n6qrlh9azzg1q68rk99h3xkbs82wq0yk6h2vb2c5r3zk"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
(define-public r-biocstyle
(package
(name "r-biocstyle")
- (version "2.10.0")
+ (version "2.12.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocStyle" version))
(sha256
(base32
- "01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31"))))
+ "029x8r9rcx6zy0xixdpwxai4jv4ynb161821fzac6z4r8k418398"))))
(properties
`((upstream-name . "BiocStyle")))
(build-system r-build-system)
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.18.0")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7"))))
+ "1gkw9s6dhdryga9ap5yhvcqg9jsy4cn417ayqk1qiv6fy91fd124"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(define-public r-s4vectors
(package
(name "r-s4vectors")
- (version "0.20.1")
+ (version "0.22.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "S4Vectors" version))
(sha256
(base32
- "18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"))))
+ "1wkqmpy0d0fab9bjfc7i5wh2zng75pg9rn9c1z1lkki7fpwaw2jb"))))
(properties
`((upstream-name . "S4Vectors")))
(build-system r-build-system)
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.16.0")
+ (version "2.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1"))))
+ "0g06y6xlm2q7p7g7phfc8qj14pqpgbb0mkyjzkfgsrwjmzvpwy6m"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.18.2")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "07bm35jcczpyxap0b3gky4b28z38z423sngzsm19d9krjxr76b5p"))))
+ "0zkhms81b3jz30q7ag81a1mq1rgqg4izyfdvcni68gvn8gm7kdyk"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-edger
(package
(name "r-edger")
- (version "3.24.3")
+ (version "3.26.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "15yimsbsxmxhlsfmgw5j7fd8qn08zz4xqxrir1c6n2dc103y22xg"))))
+ "10zhnybcwacgwcdp5p792njzl4kcafvnnnxbd7mszhxrm1sliqr8"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
(define-public r-variantannotation
(package
(name "r-variantannotation")
- (version "1.28.13")
+ (version "1.30.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "VariantAnnotation" version))
(sha256
(base32
- "1a7b0bg579ynpbfh5dk87fdgl62r9cwk4zmrl61m6zil7881p3gh"))))
+ "1sd01yv1hnwc16412ilncrrph4gxsr9ds0nqg1czl69fqaixjn1i"))))
(properties
`((upstream-name . "VariantAnnotation")))
(inputs
("r-genomicranges" ,r-genomicranges)
("r-iranges" ,r-iranges)
("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-rhtslib" ,r-rhtslib)
("r-rsamtools" ,r-rsamtools)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)
(define-public r-limma
(package
(name "r-limma")
- (version "3.38.3")
+ (version "3.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "08va8jggmv61wym955mnb1n31mgikrmjys7dl1kp5hp3yia8jg7l"))))
+ "03qxn3bs0gxq480vjd26cvhiq7jisw7kpmb3wpkrjk8jnsb10aax"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
(define-public r-xvector
(package
(name "r-xvector")
- (version "0.22.0")
+ (version "0.24.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "XVector" version))
(sha256
(base32
- "01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm"))))
+ "12y09pwy86h1za6cmaxs960r7fs0vjzhl0li8jn59vqq9liza1ap"))))
(properties
`((upstream-name . "XVector")))
(build-system r-build-system)
(define-public r-genomicranges
(package
(name "r-genomicranges")
- (version "1.34.0")
+ (version "1.36.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicRanges" version))
(sha256
(base32
- "0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"))))
+ "1285fr8qjd7d0ixpv7d5imi0n6wzc4k6yia1rkmig71qd2gg556k"))))
(properties
`((upstream-name . "GenomicRanges")))
(build-system r-build-system)
(define-public r-biobase
(package
(name "r-biobase")
- (version "2.42.0")
+ (version "2.44.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biobase" version))
(sha256
(base32
- "10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin"))))
+ "15yl92niqamx3lmwd11zlk0xniibqnh1gi280iadxicmchi83npc"))))
(properties
`((upstream-name . "Biobase")))
(build-system r-build-system)
(define-public r-annotationdbi
(package
(name "r-annotationdbi")
- (version "1.44.0")
+ (version "1.46.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationDbi" version))
(sha256
(base32
- "1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d"))))
+ "0lfq5668a6sq4kqhxx78hl3jcaqdsaaliiybl9xyya2scdk8c29c"))))
(properties
`((upstream-name . "AnnotationDbi")))
(build-system r-build-system)
(define-public r-biomart
(package
(name "r-biomart")
- (version "2.38.0")
+ (version "2.40.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biomaRt" version))
(sha256
(base32
- "1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2"))))
+ "1i457s91bn7n60bzw3zk4h64xgmawlrr6bq4z4cb7jlm04hdq8qm"))))
(properties
`((upstream-name . "biomaRt")))
(build-system r-build-system)
(define-public r-biocparallel
(package
(name "r-biocparallel")
- (version "1.16.6")
+ (version "1.18.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocParallel" version))
(sha256
(base32
- "1iv2xzm6lz371z0llhcxl8hmc5jfw0hjwnf1qc8d7jk9djgcaks2"))))
+ "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x"))))
(properties
`((upstream-name . "BiocParallel")))
(build-system r-build-system)
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.50.2")
+ (version "2.52.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "16cqqc8i6gb0jcz0lizfqqxsq7g0yb0ll2s9qzmb45brp07dg8f7"))))
+ "0inrl97hli3qz6cfxcikc4picmbrqc8phdgqi18ynlvxy5ql64h4"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(define-public r-delayedarray
(package
(name "r-delayedarray")
- (version "0.8.0")
+ (version "0.10.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "DelayedArray" version))
(sha256
(base32
- "0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f"))))
+ "0l907ggxndn3f29zvsd5pppmp4c31rb22r6zkhvgph7xdxahyy6z"))))
(properties
`((upstream-name . "DelayedArray")))
(build-system r-build-system)
("r-biocparallel" ,r-biocparallel)
("r-s4vectors" ,r-s4vectors)
("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
("r-matrixstats" ,r-matrixstats)))
(home-page "https://bioconductor.org/packages/DelayedArray")
(synopsis "Delayed operations on array-like objects")
(define-public r-summarizedexperiment
(package
(name "r-summarizedexperiment")
- (version "1.12.0")
+ (version "1.14.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "SummarizedExperiment" version))
(sha256
(base32
- "07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"))))
+ "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci"))))
(properties
`((upstream-name . "SummarizedExperiment")))
(build-system r-build-system)
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.18.1")
+ (version "1.20.0")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1maslav2r34wjyzh2nlwa862in1ir7i5xk57nw2nlfh5gqy112jd"))))
+ "13zw7bb1adgph9bf9b9y725nr0320b80y70p2yqf3bjb2klfxf55"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.34.7")
+ (version "1.34.8")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "100y8cx9xfglbn36k25y09y0qfwm0qpb4b01qhk367832rqz5dhz"))))
+ "1sxp86hdsg32l2c85jgic65gy92d8kxsm01264hrx6yikdhicjax"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
"13fv78sk5g0gqfl3ks3rps3zc1k66a4lzxvgn36r7ix43yxk7hnr"))))
(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)))
(inputs
(sha256
(base32
"0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"))))
+ (properties `((upstream-name . "RCAS")))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(define-public r-seurat
(package
(name "r-seurat")
- (version "2.3.4")
+ (version "3.0.0")
(source (origin
(method url-fetch)
(uri (cran-uri "Seurat" version))
(sha256
(base32
- "0l8bv4i9nzz26mirnva10mq6pimibj24vk7vpvfypgn7xk4942hd"))))
+ "183lm2wk0i3g114jbdf7pb4ssizr48qzqv3cknbsiackr8kvpsvc"))))
(properties `((upstream-name . "Seurat")))
(build-system r-build-system)
(propagated-inputs
`(("r-ape" ,r-ape)
("r-cluster" ,r-cluster)
("r-cowplot" ,r-cowplot)
- ("r-dosnow" ,r-dosnow)
- ("r-dplyr" ,r-dplyr)
- ("r-dtw" ,r-dtw)
("r-fitdistrplus" ,r-fitdistrplus)
- ("r-foreach" ,r-foreach)
- ("r-fpc" ,r-fpc)
+ ("r-future" ,r-future)
+ ("r-future-apply" ,r-future-apply)
("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
("r-ggridges" ,r-ggridges)
- ("r-gplots" ,r-gplots)
- ("r-hdf5r" ,r-hdf5r)
- ("r-hmisc" ,r-hmisc)
- ("r-httr" ,r-httr)
("r-ica" ,r-ica)
("r-igraph" ,r-igraph)
("r-irlba" ,r-irlba)
- ("r-lars" ,r-lars)
+ ("r-kernsmooth" ,r-kernsmooth)
("r-lmtest" ,r-lmtest)
("r-mass" ,r-mass)
("r-matrix" ,r-matrix)
("r-metap" ,r-metap)
- ("r-mixtools" ,r-mixtools)
("r-pbapply" ,r-pbapply)
("r-plotly" ,r-plotly)
("r-png" ,r-png)
("r-rcpp" ,r-rcpp)
("r-rcppeigen" ,r-rcppeigen)
("r-rcppprogress" ,r-rcppprogress)
- ("r-reshape2" ,r-reshape2)
("r-reticulate" ,r-reticulate)
+ ("r-rlang" ,r-rlang)
("r-rocr" ,r-rocr)
+ ("r-rsvd" ,r-rsvd)
("r-rtsne" ,r-rtsne)
+ ("r-scales" ,r-scales)
+ ("r-sctransform" ,r-sctransform)
("r-sdmtools" ,r-sdmtools)
- ("r-tidyr" ,r-tidyr)
("r-tsne" ,r-tsne)))
(home-page "http://www.satijalab.org/seurat")
(synopsis "Seurat is an R toolkit for single cell genomics")
(define-public r-ensembldb
(package
(name "r-ensembldb")
- (version "2.6.7")
+ (version "2.6.8")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ensembldb" version))
(sha256
(base32
- "1wqq0m1fgvgkzq5zr2s9cj2s7qkg9lx3dwwsqixzs5fn52p4dn7f"))))
+ "0gijx2l2y00h6gfj3gfr7rd4vva6qf2vkfdfy5gdmvqlxy84ka38"))))
(build-system r-build-system)
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
(base32
"0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934"))))
(build-system r-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;; See https://github.com/tengfei/ggbio/issues/117
+ ;; This fix will be included in the next release.
+ (add-after 'unpack 'fix-typo
+ (lambda _
+ (substitute* "R/GGbio-class.R"
+ (("fechable") "fetchable"))
+ #t)))))
(propagated-inputs
`(("r-annotationdbi" ,r-annotationdbi)
("r-annotationfilter" ,r-annotationfilter)
(define-public r-ldblock
(package
(name "r-ldblock")
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ldblock" version))
(sha256
(base32
- "0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips"))))
+ "01lf74pby7si2g3kgc10qzr6lkcbigqcgqs2j3anc38vzxv0zhwv"))))
(build-system r-build-system)
(propagated-inputs
`(("r-biocgenerics" ,r-biocgenerics)
single-cell RNA-seq data.")
(license license:bsd-3)))
+;; pigx-scrnaseq does not work with the latest version of loompy.
+(define-public python-loompy-for-pigx-scrnaseq
+ (package (inherit python-loompy)
+ (name "python-loompy")
+ (version "2.0.3")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/linnarsson-lab/loompy.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0pjyl532pl8sbv71yci6h0agchn0naw2qjcwj50n6afrsahbsag3"))))
+ ;; There are none.
+ (arguments '(#:tests? #f))))
+
;; We cannot use the latest commit because it requires Java 9.
(define-public java-forester
(let ((commit "86b07efe302d5094b42deed9260f719a4c4ac2e6")
("python-pandas" ,python-pandas)
("python-magic" ,python-magic)
("python-numpy" ,python-numpy)
- ("python-loompy" ,python-loompy)
+ ("python-loompy" ,python-loompy-for-pigx-scrnaseq)
("ghc-pandoc" ,ghc-pandoc)
("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc)
("samtools" ,samtools)
Additionally, the AdapterRemoval may be used to recover a consensus adapter
sequence for paired-ended data, for which this information is not available.")
(license license:gpl3+)))
+
+(define-public pplacer
+ (let ((commit "807f6f3"))
+ (package
+ (name "pplacer")
+ ;; The commit should be updated with each version change.
+ (version "1.1.alpha19")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/matsen/pplacer.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "11ppbbbx20p2g9wj3ff64dhnarb12q79v7qh4rk0gj6lkbz4n7cn"))))
+ (build-system ocaml-build-system)
+ (arguments
+ `(#:modules ((guix build ocaml-build-system)
+ (guix build utils)
+ (ice-9 ftw))
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-after 'unpack 'fix-build-with-latest-ocaml
+ (lambda _
+ (substitute* "myocamlbuild.ml"
+ (("dep \\[\"c_pam\"\\]" m)
+ (string-append "flag [\"ocaml\"; \"compile\"] (A \"-unsafe-string\");\n"
+ m))
+ (("let run_and_read" m)
+ (string-append "
+let split s ch =
+ let x = ref [] in
+ let rec go s =
+ let pos = String.index s ch in
+ x := (String.before s pos)::!x;
+ go (String.after s (pos + 1))
+ in
+ try go s
+ with Not_found -> !x
+let split_nl s = split s '\\n'
+let before_space s =
+ try String.before s (String.index s ' ')
+ with Not_found -> s
+
+" m))
+ (("run_and_read \"ocamlfind list \\| cut -d' ' -f1\"" m)
+ (string-append "List.map before_space (split_nl & " m ")"))
+ ((" blank_sep_strings &") "")
+ ((" Lexing.from_string &") ""))
+ #t))
+ (add-after 'unpack 'replace-bundled-cddlib
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((cddlib-src (assoc-ref inputs "cddlib-src"))
+ (local-dir "cddlib_guix"))
+ (mkdir local-dir)
+ (with-directory-excursion local-dir
+ (invoke "tar" "xvf" cddlib-src))
+ (let ((cddlib-src-folder
+ (string-append local-dir "/"
+ (list-ref (scandir local-dir) 2)
+ "/lib-src")))
+ (for-each make-file-writable (find-files "cdd_src" ".*"))
+ (for-each
+ (lambda (file)
+ (copy-file file
+ (string-append "cdd_src/" (basename file))))
+ (find-files cddlib-src-folder ".*[ch]$")))
+ #t)))
+ (add-after 'unpack 'fix-makefile
+ (lambda _
+ ;; Remove system calls to 'git'.
+ (substitute* "Makefile"
+ (("^DESCRIPT:=pplacer-.*")
+ (string-append
+ "DESCRIPT:=pplacer-$(shell uname)-v" ,version "\n")))
+ (substitute* "myocamlbuild.ml"
+ (("git describe --tags --long .*\\\" with")
+ (string-append
+ "echo -n v" ,version "-" ,commit "\" with")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (copy-recursively "bin" bin))
+ #t)))))
+ (inputs
+ `(("zlib" ,zlib "static")
+ ("gsl" ,gsl)
+ ("ocaml-ounit" ,ocaml-ounit)
+ ("ocaml-batteries" ,ocaml-batteries)
+ ("ocaml-camlzip" ,camlzip)
+ ("ocaml-csv" ,ocaml-csv)
+ ("ocaml-sqlite3" ,ocaml-sqlite3)
+ ("ocaml-xmlm" ,ocaml-xmlm)
+ ("ocaml-mcl" ,ocaml-mcl)
+ ("ocaml-gsl" ,ocaml-gsl-1)))
+ (native-inputs
+ `(("cddlib-src" ,(package-source cddlib))
+ ("ocamlbuild" ,ocamlbuild)
+ ("pkg-config" ,pkg-config)))
+ (propagated-inputs
+ `(("pplacer-scripts" ,pplacer-scripts)))
+ (synopsis "Phylogenetic placement of biological sequences")
+ (description
+ "Pplacer places query sequences on a fixed reference phylogenetic tree
+to maximize phylogenetic likelihood or posterior probability according to a
+reference alignment. Pplacer is designed to be fast, to give useful
+information about uncertainty, and to offer advanced visualization and
+downstream analysis.")
+ (home-page "http://matsen.fhcrc.org/pplacer")
+ (license license:gpl3))))
+
+;; This package is installed alongside 'pplacer'. It is a separate package so
+;; that it can use the python-build-system for the scripts that are
+;; distributed alongside the main OCaml binaries.
+(define pplacer-scripts
+ (package
+ (inherit pplacer)
+ (name "pplacer-scripts")
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-scripts-dir
+ (lambda _ (chdir "scripts") #t))
+ (replace 'check
+ (lambda _ (invoke "python" "-m" "unittest" "discover" "-v") #t))
+ (add-after 'install 'wrap-executables
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (let ((path (string-append
+ (assoc-ref inputs "hmmer") "/bin:"
+ (assoc-ref inputs "infernal") "/bin")))
+ (display path)
+ (wrap-program (string-append bin "/refpkg_align.py")
+ `("PATH" ":" prefix (,path))))
+ (let ((path (string-append
+ (assoc-ref inputs "hmmer") "/bin")))
+ (wrap-program (string-append bin "/hrefpkg_query.py")
+ `("PATH" ":" prefix (,path)))))
+ #t)))))
+ (inputs
+ `(("infernal" ,infernal)
+ ("hmmer" ,hmmer)))
+ (propagated-inputs
+ `(("python-biopython" ,python2-biopython)
+ ("taxtastic" ,taxtastic)))
+ (synopsis "Pplacer Python scripts")))
+
+(define-public python2-checkm-genome
+ (package
+ (name "python2-checkm-genome")
+ (version "1.0.13")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "checkm-genome" version))
+ (sha256
+ (base32
+ "0bm8gpxjmzxsxxl8lzwqhgx8g1dlnmp6znz7wv3hgb0gdjbf9dzz"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f)) ; some tests are interactive
+ (propagated-inputs
+ `(("python-dendropy" ,python2-dendropy)
+ ("python-matplotlib" ,python2-matplotlib)
+ ("python-numpy" ,python2-numpy)
+ ("python-pysam" ,python2-pysam)
+ ("python-scipy" ,python2-scipy)))
+ (home-page "http://pypi.python.org/pypi/checkm/")
+ (synopsis "Assess the quality of putative genome bins")
+ (description
+ "CheckM provides a set of tools for assessing the quality of genomes
+recovered from isolates, single cells, or metagenomes. It provides robust
+estimates of genome completeness and contamination by using collocated sets of
+genes that are ubiquitous and single-copy within a phylogenetic lineage.
+Assessment of genome quality can also be examined using plots depicting key
+genomic characteristics (e.g., GC, coding density) which highlight sequences
+outside the expected distributions of a typical genome. CheckM also provides
+tools for identifying genome bins that are likely candidates for merging based
+on marker set compatibility, similarity in genomic characteristics, and
+proximity within a reference genome.")
+ (license license:gpl3+)))
+
+(define-public umi-tools
+ (package
+ (name "umi-tools")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "umi_tools" version))
+ (sha256
+ (base32
+ "08y3vz1vcx09whmbsn722lcs6jl9wyrh9i4p3k8j4cb1i32bij4a"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-setuptools" ,python-setuptools)
+ ("python-pandas" ,python-pandas)
+ ("python-future" ,python-future)
+ ("python-scipy" ,python-scipy)
+ ("python-matplotlib" ,python-matplotlib)
+ ("python-regex" ,python-regex)
+ ("python-pysam" ,python-pysam)))
+ (native-inputs
+ `(("python-setuptools" ,python-setuptools)
+ ("python-cython" ,python-cython)))
+ (home-page "https://github.com/CGATOxford/UMI-tools")
+ (synopsis "Tools for analyzing unique modular identifiers")
+ (description "This package provides tools for dealing with @dfn{Unique
+Molecular Identifiers} (UMIs) and @dfn{Random Molecular Tags} (RMTs) in
+genetic sequences. There are six tools: the @code{extract} and
+@code{whitelist} commands are used to prepare a fastq containg UMIs @code{+/-}
+cell barcodes for alignment. The remaining commands, @code{group},
+@code{dedup}, and @{count}/@code{count_tab}, are used to identify PCR
+duplicates using the UMIs and perform different levels of analysis depending
+on the needs of the user.")
+ (license license:expat)))
HCoop / jackhill / guix / guix.git / blobdiff