(define-public delly
(package
(name "delly")
- (version "0.7.9")
+ (version "0.8.3")
(source (origin
(method git-fetch)
(uri (git-reference
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+ (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
(modules '((guix build utils)))
(snippet
'(begin
#t))))))
(inputs
`(("boost" ,boost)
+ ("bzip2" ,bzip2)
("htslib" ,htslib)
- ("zlib" ,zlib)
- ("bzip2" ,bzip2)))
+ ("zlib" ,zlib)))
(home-page "https://github.com/dellytools/delly")
(synopsis "Integrated structural variant prediction method")
(description "Delly is an integrated structural variant prediction method
(define-public seqmagick
(package
(name "seqmagick")
- (version "0.7.0")
+ (version "0.8.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "seqmagick" version))
(sha256
(base32
- "12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
+ "0pf98da7i59q47gwrbx0wjk6xlvbybiwphw80w7h4ydjj0579a2b"))))
(build-system python-build-system)
(inputs
`(("python-biopython" ,python-biopython)))
throughput genetic sequencing data sets using regression methods.")
(license license:artistic2.0)))
-(define-public r-qtl
- (package
- (name "r-qtl")
- (version "1.46-2")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "mirror://cran/src/contrib/qtl_"
- version ".tar.gz"))
- (sha256
- (base32
- "0rbwcnvyy96gq1dsgpxx03pv423qya26h6ws5y0blj3blfdmj83a"))))
- (build-system r-build-system)
- (home-page "https://rqtl.org/")
- (synopsis "R package for analyzing QTL experiments in genetics")
- (description "R/qtl is an extension library for the R statistics
-system. It is used to analyze experimental crosses for identifying
-genes contributing to variation in quantitative traits (so-called
-quantitative trait loci, QTLs).
-
-Using a hidden Markov model, R/qtl estimates genetic maps, to
-identify genotyping errors, and to perform single-QTL and two-QTL,
-two-dimensional genome scans.")
- (license license:gpl3)))
-
-(define-public r-qtl2
- (package
- (name "r-qtl2")
- (version "0.22-11")
- (source (origin
- (method url-fetch)
- (uri (cran-uri "qtl2" version))
- (sha256
- (base32 "0dfdzjylqzc92dcszawc8cyinxccjm3p36v9vcq9ma818pqcanmr"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-jsonlite" ,r-jsonlite)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rsqlite" ,r-rsqlite)
- ("r-yaml" ,r-yaml)))
- (home-page "https://kbroman.org/qtl2/")
- (synopsis "Quantitative Trait Locus Mapping in Experimental Crosses")
- (description
- "This package provides a set of tools to perform @dfn{Quantitative Trait
-Locus} (QTL) analysis in experimental crosses. It is a reimplementation of the
-@code{R/qtl} package to better handle high-dimensional data and complex cross
-designs. Broman et al. (2018) <doi:10.1534/genetics.118.301595>.")
- (license license:gpl3)))
-
(define-public r-zlibbioc
(package
(name "r-zlibbioc")
unmodeled, or latent sources of noise.")
(license license:artistic2.0)))
-(define-public r-seqminer
- (package
- (name "r-seqminer")
- (version "8.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "seqminer" version))
- (sha256
- (base32
- "00jzj8mwb0zaiwlifd41b26mrq9mzigj18nc29dydi0r42hxg16i"))))
- (build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
- (home-page "http://seqminer.genomic.codes")
- (synopsis "Read nucleotide sequence data (VCF, BCF, and METAL formats)")
- (description
- "This package provides tools to integrate nucleotide sequencing
-data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.")
- ;; Any version of the GPL is acceptable
- (license (list license:gpl2+ license:gpl3+))))
-
(define-public r-raremetals2
(package
(name "r-raremetals2")
trait.")
(license license:gpl3)))
-(define-public r-maldiquant
- (package
- (name "r-maldiquant")
- (version "1.19.3")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "MALDIquant" version))
- (sha256
- (base32
- "0b7kdz3x4sdq413h1q09l1qhcvdnnwv6fqsqwllks1cd3xy34c57"))))
- (properties `((upstream-name . "MALDIquant")))
- (build-system r-build-system)
- (home-page "https://cran.r-project.org/web/packages/MALDIquant")
- (synopsis "Quantitative analysis of mass spectrometry data")
- (description
- "This package provides a complete analysis pipeline for matrix-assisted
-laser desorption/ionization-time-of-flight (MALDI-TOF) and other
-two-dimensional mass spectrometry data. In addition to commonly used plotting
-and processing methods it includes distinctive features, namely baseline
-subtraction methods such as morphological filters (TopHat) or the
-statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak
-alignment using warping functions, handling of replicated measurements as well
-as allowing spectra with different resolutions.")
- (license license:gpl3+)))
-
(define-public r-protgenerics
(package
(name "r-protgenerics")
and irregular enzymatic cleavages, mass measurement accuracy, etc.")
(license license:artistic2.0)))
-(define-public r-seurat
- (package
- (name "r-seurat")
- (version "3.2.0")
- (source (origin
- (method url-fetch)
- (uri (cran-uri "Seurat" version))
- (sha256
- (base32
- "1vj3dlsqakgnn4x1jz9fkl2cy0jzc5s65h1c20fnamr7lk45pnf2"))))
- (properties `((upstream-name . "Seurat")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-cluster" ,r-cluster)
- ("r-cowplot" ,r-cowplot)
- ("r-fitdistrplus" ,r-fitdistrplus)
- ("r-future" ,r-future)
- ("r-future-apply" ,r-future-apply)
- ("r-ggplot2" ,r-ggplot2)
- ("r-ggrepel" ,r-ggrepel)
- ("r-ggridges" ,r-ggridges)
- ("r-httr" ,r-httr)
- ("r-ica" ,r-ica)
- ("r-igraph" ,r-igraph)
- ("r-irlba" ,r-irlba)
- ("r-jsonlite" ,r-jsonlite)
- ("r-kernsmooth" ,r-kernsmooth)
- ("r-leiden" ,r-leiden)
- ("r-lmtest" ,r-lmtest)
- ("r-mass" ,r-mass)
- ("r-matrix" ,r-matrix)
- ("r-miniui" ,r-miniui)
- ("r-patchwork" ,r-patchwork)
- ("r-pbapply" ,r-pbapply)
- ("r-plotly" ,r-plotly)
- ("r-png" ,r-png)
- ("r-rann" ,r-rann)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rcpp" ,r-rcpp)
- ("r-rcppannoy" ,r-rcppannoy)
- ("r-rcppeigen" ,r-rcppeigen)
- ("r-rcppprogress" ,r-rcppprogress)
- ("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-shiny" ,r-shiny)
- ("r-spatstat" ,r-spatstat)
- ("r-tibble" ,r-tibble)
- ("r-uwot" ,r-uwot)))
- (home-page "http://www.satijalab.org/seurat")
- (synopsis "Seurat is an R toolkit for single cell genomics")
- (description
- "This package is an R package designed for QC, analysis, and
-exploration of single cell RNA-seq data. It easily enables widely-used
-analytical techniques, including the identification of highly variable genes,
-dimensionality reduction; PCA, ICA, t-SNE, standard unsupervised clustering
-algorithms; density clustering, hierarchical clustering, k-means, and the
-discovery of differentially expressed genes and markers.")
- (license license:gpl3)))
-
(define-public r-aroma-light
(package
(name "r-aroma-light")
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "2.4.2")
+ (version "2.4.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "01jxxwxhf9n8baxgja4rb592p5210s4ppd7a5b4xby5aalhzkr0l"))))
+ "1gx0hzrkla92pgmfkrm2zp0ccnhizq6rs26zgzpi5x8a5lvghh5q"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
visualizations for publication-quality multi-panel figures.")
(license license:gpl2+)))
-(define-public r-fithic
- (package
- (name "r-fithic")
- (version "1.14.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "FitHiC" version))
- (sha256
- (base32
- "1dffkdxm08wq4kjd9j2v2625x3p6vbrk33a2zx94pwpgkghr72yp"))))
- (properties `((upstream-name . "FitHiC")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-data-table" ,r-data-table)
- ("r-fdrtool" ,r-fdrtool)
- ("r-rcpp" ,r-rcpp)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/FitHiC")
- (synopsis "Confidence estimation for intra-chromosomal contact maps")
- (description
- "Fit-Hi-C is a tool for assigning statistical confidence estimates to
-intra-chromosomal contact maps produced by genome-wide genome architecture
-assays such as Hi-C.")
- (license license:gpl2+)))
-
-(define-public r-hitc
- (package
- (name "r-hitc")
- (version "1.32.0")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "HiTC" version))
- (sha256
- (base32
- "1jx2pfa7sbdz7xi466lz1h5xv126g56z73n0a5l2wrq28k47qaxy"))))
- (properties `((upstream-name . "HiTC")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biostrings" ,r-biostrings)
- ("r-genomeinfodb" ,r-genomeinfodb)
- ("r-genomicranges" ,r-genomicranges)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-rcolorbrewer" ,r-rcolorbrewer)
- ("r-rtracklayer" ,r-rtracklayer)))
- (home-page "https://bioconductor.org/packages/HiTC")
- (synopsis "High throughput chromosome conformation capture analysis")
- (description
- "The HiTC package was developed to explore high-throughput \"C\" data
-such as 5C or Hi-C. Dedicated R classes as well as standard methods for
-quality controls, normalization, visualization, and further analysis are also
-provided.")
- (license license:artistic2.0)))
-
-(define-public r-hdf5array
- (package
- (name "r-hdf5array")
- (version "1.16.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "HDF5Array" version))
- (sha256
- (base32
- "01767v90nl0499jcicpxngbbs0af5p9c5aasi5va01w3v5bnqddn"))))
- (properties `((upstream-name . "HDF5Array")))
- (build-system r-build-system)
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("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)))
- (home-page "https://bioconductor.org/packages/HDF5Array")
- (synopsis "HDF5 back end for DelayedArray objects")
- (description "This package provides an array-like container for convenient
-access and manipulation of HDF5 datasets. It supports delayed operations and
-block processing.")
- (license license:artistic2.0)))
-
-(define-public r-rhdf5lib
- (package
- (name "r-rhdf5lib")
- (version "1.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "Rhdf5lib" version))
- (sha256
- (base32
- "0f45sqrvzj6x4mckalyp8366hm8v0rrmzklx3xd4gs6l2wallcn9"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- ;; Delete bundled binaries
- (delete-file-recursively "src/wininclude/")
- (delete-file-recursively "src/winlib-4.9.3/")
- (delete-file-recursively "src/winlib-8.3.0/")
- (delete-file "src/hdf5small_cxx_hl_1.10.6.tar.gz")
- #t))))
- (properties `((upstream-name . "Rhdf5lib")))
- (build-system r-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'do-not-use-bundled-hdf5
- (lambda* (#:key inputs #:allow-other-keys)
- (for-each delete-file '("configure" "configure.ac"))
- ;; Do not make other packages link with the proprietary libsz.
- (substitute* "R/zzz.R"
- ((" \"%s/libsz.a\"") ""))
- (with-directory-excursion "src"
- (invoke "tar" "xvf" (assoc-ref inputs "hdf5-source"))
- (rename-file (string-append "hdf5-" ,(package-version hdf5-1.10))
- "hdf5")
- ;; Remove timestamp and host system information to make
- ;; the build reproducible.
- (substitute* "hdf5/src/libhdf5.settings.in"
- (("Configured on: @CONFIG_DATE@")
- "Configured on: Guix")
- (("Uname information:.*")
- "Uname information: Linux\n")
- ;; Remove unnecessary store reference.
- (("C Compiler:.*")
- "C Compiler: GCC\n"))
- (rename-file "Makevars.in" "Makevars")
- (substitute* "Makevars"
- (("@ZLIB_LIB@") "-lz")
- (("@ZLIB_INCLUDE@") "")
- (("HDF5_CXX_LIB=.*")
- (string-append "HDF5_CXX_LIB="
- (assoc-ref inputs "hdf5") "/lib/libhdf5_cpp.a\n"))
- (("HDF5_LIB=.*")
- (string-append "HDF5_LIB="
- (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")))
- #t)))))
- (inputs
- `(("zlib" ,zlib)))
- (propagated-inputs
- `(("hdf5" ,hdf5-1.10)))
- (native-inputs
- `(("hdf5-source" ,(package-source hdf5-1.10))
- ("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/Rhdf5lib")
- (synopsis "HDF5 library as an R package")
- (description "This package provides C and C++ HDF5 libraries for use in R
-packages.")
- (license license:artistic2.0)))
-
-(define-public r-beachmat
- (package
- (name "r-beachmat")
- (version "2.4.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "beachmat" version))
- (sha256
- (base32
- "1vl6jbf9ia78cm4ikdb8vz04jv4b46zhvg5i006c63a9pzw7zhxi"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-delayedarray" ,r-delayedarray)
- ("r-matrix" ,r-matrix)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (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
-variety of commonly used matrix types, including sparse and HDF5-backed
-matrices.")
- (license license:gpl3)))
-
-(define-public r-singlecellexperiment
- (package
- (name "r-singlecellexperiment")
- (version "1.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "SingleCellExperiment" version))
- (sha256
- (base32
- "092wvk11n7pa234vlwhxm3gdi4k3sbnz1splhxalbdhz3jf02zfp"))))
- (properties
- `((upstream-name . "SingleCellExperiment")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocgenerics" ,r-biocgenerics)
- ("r-s4vectors" ,r-s4vectors)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/SingleCellExperiment")
- (synopsis "S4 classes for single cell data")
- (description "This package defines an S4 class for storing data from
-single-cell experiments. This includes specialized methods to store and
-retrieve spike-in information, dimensionality reduction coordinates and size
-factors for each cell, along with the usual metadata for genes and
-libraries.")
- (license license:gpl3)))
-
-(define-public r-scater
- (package
- (name "r-scater")
- (version "1.16.2")
- (source (origin
- (method url-fetch)
- (uri (bioconductor-uri "scater" version))
- (sha256
- (base32
- "1pa5wvgjb30rw1vsjwbnn07ss3sc5n8ck5d7khdby4r2s9177s33"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-ggbeeswarm" ,r-ggbeeswarm)
- ("r-ggplot2" ,r-ggplot2)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-rlang" ,r-rlang)
- ("r-s4vectors" ,r-s4vectors)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-summarizedexperiment" ,r-summarizedexperiment)
- ("r-viridis" ,r-viridis)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/davismcc/scater")
- (synopsis "Single-cell analysis toolkit for gene expression data in R")
- (description "This package provides a collection of tools for doing
-various analyses of single-cell RNA-seq gene expression data, with a focus on
-quality control.")
- (license license:gpl2+)))
-
-(define-public r-scran
- (package
- (name "r-scran")
- (version "1.16.0")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "scran" version))
- (sha256
- (base32
- "1gm4ys4aq8h1pn45k1rxk384wjyf55izivw8kgxbrflj6j4xvvsv"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-beachmat" ,r-beachmat)
- ("r-bh" ,r-bh)
- ("r-biocgenerics" ,r-biocgenerics)
- ("r-biocneighbors" ,r-biocneighbors)
- ("r-biocparallel" ,r-biocparallel)
- ("r-biocsingular" ,r-biocsingular)
- ("r-delayedarray" ,r-delayedarray)
- ("r-delayedmatrixstats" ,r-delayedmatrixstats)
- ("r-dqrng" ,r-dqrng)
- ("r-edger" ,r-edger)
- ("r-igraph" ,r-igraph)
- ("r-iranges" ,r-iranges)
- ("r-limma" ,r-limma)
- ("r-matrix" ,r-matrix)
- ("r-rcpp" ,r-rcpp)
- ("r-s4vectors" ,r-s4vectors)
- ("r-scater" ,r-scater)
- ("r-singlecellexperiment" ,r-singlecellexperiment)
- ("r-statmod" ,r-statmod)
- ("r-summarizedexperiment" ,r-summarizedexperiment)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://bioconductor.org/packages/scran")
- (synopsis "Methods for single-cell RNA-Seq data analysis")
- (description "This package implements a variety of low-level analyses of
-single-cell RNA-seq data. Methods are provided for normalization of
-cell-specific biases, assignment of cell cycle phase, and detection of highly
-variable and significantly correlated genes.")
- (license license:gpl3)))
-
-(define-public r-delayedmatrixstats
- (package
- (name "r-delayedmatrixstats")
- (version "1.10.1")
- (source
- (origin
- (method url-fetch)
- (uri (bioconductor-uri "DelayedMatrixStats" version))
- (sha256
- (base32
- "046sam0rz42ph0m7jz7v3bck7d3h2mp45gzywh5dvc1qkjq6fdxx"))))
- (properties
- `((upstream-name . "DelayedMatrixStats")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biocparallel" ,r-biocparallel)
- ("r-delayedarray" ,r-delayedarray)
- ("r-hdf5array" ,r-hdf5array)
- ("r-iranges" ,r-iranges)
- ("r-matrix" ,r-matrix)
- ("r-matrixstats" ,r-matrixstats)
- ("r-s4vectors" ,r-s4vectors)))
- (native-inputs
- `(("r-knitr" ,r-knitr)))
- (home-page "https://github.com/PeteHaitch/DelayedMatrixStats")
- (synopsis "Functions that apply to rows and columns of DelayedMatrix objects")
- (description
- "This package provides a port of the @code{matrixStats} API for use with
-@code{DelayedMatrix} objects from the @code{DelayedArray} package. It
-contains high-performing functions operating on rows and columns of
-@code{DelayedMatrix} objects, e.g. @code{colMedians}, @code{rowMedians},
-@code{colRanks}, @code{rowRanks}, @code{colSds}, and @code{rowSds}. Functions
-are optimized per data type and for subsetted calculations such that both
-memory usage and processing time is minimized.")
- (license license:expat)))
-
-(define-public r-phangorn
- (package
- (name "r-phangorn")
- (version "2.5.5")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "phangorn" version))
- (sha256
- (base32
- "0ihkaykqjmf80d8wrk3saphxvnv58zma6pd13633bd3cwanc33f5"))))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-fastmatch" ,r-fastmatch)
- ("r-igraph" ,r-igraph)
- ("r-magrittr" ,r-magrittr)
- ("r-matrix" ,r-matrix)
- ("r-quadprog" ,r-quadprog)
- ("r-rcpp" ,r-rcpp)))
- (home-page "https://github.com/KlausVigo/phangorn")
- (synopsis "Phylogenetic analysis in R")
- (description
- "Phangorn is a package for phylogenetic analysis in R. It supports
-estimation of phylogenetic trees and networks using Maximum Likelihood,
-Maximum Parsimony, distance methods and Hadamard conjugation.")
- (license license:gpl2+)))
-
(define-public r-dropbead
(let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
(revision "2"))
(supported-systems '("x86_64-linux"))
(license license:bsd-3))))
-(define-public r-diversitree
- (package
- (name "r-diversitree")
- (version "0.9-13")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "diversitree" version))
- (sha256
- (base32
- "00vi4klywi35hd170ksjv3xja3hqqbkcidcnrrlpgv4179k0azix"))))
- (build-system r-build-system)
- (native-inputs
- `(("gfortran" ,gfortran)))
- (inputs `(("fftw" ,fftw) ("gsl" ,gsl)))
- (propagated-inputs
- `(("r-ape" ,r-ape)
- ("r-desolve" ,r-desolve)
- ("r-rcpp" ,r-rcpp)
- ("r-subplex" ,r-subplex)))
- (home-page "https://www.zoology.ubc.ca/prog/diversitree")
- (synopsis "Comparative 'phylogenetic' analyses of diversification")
- (description "This package contains a number of comparative \"phylogenetic\"
-methods, mostly focusing on analysing diversification and character evolution.
-Contains implementations of \"BiSSE\" (Binary State Speciation and Extinction)
-and its unresolved tree extensions, \"MuSSE\" (Multiple State Speciation and
-Extinction), \"QuaSSE\", \"GeoSSE\", and \"BiSSE-ness\" Other included methods
-include Markov models of discrete and continuous trait evolution and constant
-rate speciation and extinction.")
- (license license:gpl2+)))
-
(define-public sjcount
;; There is no tag for version 3.2, nor is there a release archive.
(let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
of the Hierarchical Data Format (HDF5) standard.")
(license license:expat))))
-(define-public r-absfiltergsea
- (package
- (name "r-absfiltergsea")
- (version "1.5.1")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "AbsFilterGSEA" version))
- (sha256
- (base32 "15srxkxsvn38kd5frdrwfdf0ad8gskrd0h01wmdf9hglq8fjrp7w"))))
- (properties `((upstream-name . "AbsFilterGSEA")))
- (build-system r-build-system)
- (propagated-inputs
- `(("r-biobase" ,r-biobase)
- ("r-deseq" ,r-deseq)
- ("r-limma" ,r-limma)
- ("r-rcpp" ,r-rcpp)
- ("r-rcpparmadillo" ,r-rcpparmadillo)))
- (home-page "https://cran.r-project.org/web/packages/AbsFilterGSEA/")
- (synopsis "Improved false positive control of gene-permuting with absolute filtering")
- (description
- "This package provides a function that performs gene-permuting of a gene-set
-enrichment analysis (GSEA) calculation with or without the absolute filtering.
- Without filtering, users can perform (original) two-tailed or one-tailed
-absolute GSEA.")
- (license license:gpl2)))
-
(define-public jamm
(package
(name "jamm")
(string-append "HTS_LIB=" htslib-ref "/lib/libhts.a")
(string-append "INCLUDES= -I" htslib-ref "/include/htslib")
"HTS_HEADERS=" ; No need to check for headers here.
- (string-append "LIBPATH=-L. -L" htslib-ref "/include")))))
+ (string-append "LIBPATH=-L. -L" htslib-ref "/include"))
+ (invoke "g++" "-shared" "-o" "libtabixpp.so" "tabix.o" "-lhts")
+ (invoke "ar" "rcs" "libtabixpp.a" "tabix.o"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "tabix++" bin))
- #t)))))
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib"))
+ (bin (string-append out "/bin")))
+ (install-file "tabix++" bin)
+ (install-file "libtabixpp.so" lib)
+ (install-file "libtabixpp.a" lib)
+ (install-file "tabix.hpp" (string-append out "/include"))
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/tabixpp.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include~@
+ ~@
+ ~@
+ Name: libtabixpp~@
+ Version: ~a~@
+ Description: C++ wrapper around tabix project~@
+ Libs: -L${libdir} -ltabixpp~@
+ Cflags: -I${includedir}~%"
+ out ,version)))
+ #t))))))
(home-page "https://github.com/ekg/tabixpp")
(synopsis "C++ wrapper around tabix project")
(description "This is a C++ wrapper around the Tabix project which abstracts
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "Makefile"
+ (("-c ") "-c -fPIC "))
+ #t))
+ (add-after 'build 'build-dynamic
+ (lambda _
+ (invoke "g++"
+ "-shared" "-o" "libsmithwaterman.so"
+ "smithwaterman.o" "SmithWatermanGotoh.o"
+ "disorder.o" "BandedSmithWaterman.o"
+ "LeftAlign.o" "Repeats.o" "IndelAllele.o")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(bin (string-append out "/bin"))
(lib (string-append out "/lib")))
(install-file "smithwaterman" bin)
- (install-file "libsw.a" lib))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/include/smithwaterman")))
+ (find-files "." "\\.h$"))
+ (install-file "libsmithwaterman.so" lib)
+ (install-file "libsw.a" lib)
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/smithwaterman.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include/smithwaterman~@
+ ~@
+ ~@
+ Name: smithwaterman~@
+ Version: ~a~@
+ Description: smith-waterman-gotoh alignment algorithm~@
+ Libs: -L${libdir} -lsmithwaterman~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(home-page "https://github.com/ekg/smithwaterman")
(synopsis "Implementation of the Smith-Waterman algorithm")
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
+ (add-after 'unpack 'patch-source
+ (lambda _
+ (substitute* "Makefile"
+ (("-c ") "-c -fPIC "))
+ #t))
+ (add-after 'build 'build-dynamic
+ (lambda _
+ (invoke "g++"
+ "-shared" "-o" "libfastahack.so"
+ "Fasta.o" "FastaHack.o" "split.o" "disorder.o")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
- (install-file "fastahack" bin))
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib"))
+ (bin (string-append out "/bin")))
+ (mkdir-p (string-append out "/include/fastahack"))
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/include/fastahack")))
+ (find-files "." "\\.h$"))
+ (install-file "fastahack" bin)
+ (install-file "libfastahack.so" lib)
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/fastahack.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include/fastahack~@
+ ~@
+ ~@
+ Name: fastahack~@
+ Version: ~a~@
+ Description: Indexing and sequence extraction from FASTA files~@
+ Libs: -L${libdir} -lfastahack~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(home-page "https://github.com/ekg/fastahack")
(synopsis "Indexing and sequence extraction from FASTA files")
"/vcflib-" version "-src.tar.gz"))
(sha256
(base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm"))
+ (patches (search-patches "vcflib-use-shared-libraries.patch"))
(modules '((guix build utils)))
(snippet
`(begin
+ (substitute* (find-files "." "\\.(h|c)(pp)?$")
+ (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>")
+ (("\"convert.h\"") "<smithwaterman/convert.h>")
+ (("\"disorder.h\"") "<smithwaterman/disorder.h>")
+ (("\"tabix.hpp\"") "<tabix.hpp>")
+ (("\"Fasta.h\"") "<fastahack/Fasta.h>"))
(for-each delete-file-recursively
'("fastahack" "filevercmp" "fsom" "googletest" "intervaltree"
"libVCFH" "multichoose" "smithwaterman" "tabixpp"))
(build-system gnu-build-system)
(inputs
`(("htslib" ,htslib)
+ ("fastahack" ,fastahack)
("perl" ,perl)
("python" ,python)
+ ("smithwaterman" ,smithwaterman)
+ ("tabixpp" ,tabixpp)
+ ("xz" ,xz)
("zlib" ,zlib)))
(native-inputs
- `(;; Submodules.
+ `(("pkg-config" ,pkg-config)
+ ;; Submodules.
;; This package builds against the .o files so we need to extract the source.
- ("fastahack-src" ,(package-source fastahack))
("filevercmp-src" ,(package-source filevercmp))
- ("fsom-src" ,(package-source fsom))
("intervaltree-src" ,(package-source intervaltree))
- ("multichoose-src" ,(package-source multichoose))
- ("smithwaterman-src" ,(package-source smithwaterman))
- ("tabixpp-src" ,(package-source tabixpp))))
+ ("multichoose-src" ,(package-source multichoose))))
(arguments
`(#:tests? #f ; no tests
- #:make-flags (list (string-append "HTS_LIB="
- (assoc-ref %build-inputs "htslib")
- "/lib/libhts.a")
- (string-append "HTS_INCLUDES= -I"
- (assoc-ref %build-inputs "htslib")
- "/include/htslib")
- (string-append "HTS_LDFLAGS= -L"
- (assoc-ref %build-inputs "htslib")
- "/include/htslib" " -lhts"))
#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'set-flags
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("LDFLAGS =")
+ (string-append "LDFLAGS = -Wl,-rpath="
+ (assoc-ref outputs "out") "/lib ")))
+ (substitute* "filevercmp/Makefile"
+ (("-c") "-c -fPIC"))
+ #t))
(delete 'configure)
- (delete 'check)
(add-after 'unpack 'unpack-submodule-sources
(lambda* (#:key inputs #:allow-other-keys)
(let ((unpack (lambda (source target)
(assoc-ref inputs source)
"--strip-components=1"))))))
(and
- (unpack "fastahack-src" "fastahack")
(unpack "filevercmp-src" "filevercmp")
- (unpack "fsom-src" "fsom")
(unpack "intervaltree-src" "intervaltree")
- (unpack "multichoose-src" "multichoose")
- (unpack "smithwaterman-src" "smithwaterman")
- (unpack "tabixpp-src" "tabixpp")))))
- (replace 'build
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (let ((htslib (assoc-ref inputs "htslib")))
- (with-directory-excursion "tabixpp"
- (substitute* "Makefile"
- (("-Ihtslib") (string-append "-I" htslib "/include/htslib"))
- (("-Lhtslib") (string-append "-L" htslib "/lib/htslib"))
- (("htslib/htslib") (string-append htslib "/include/htslib")))
- (invoke "make"
- (string-append "HTS_LIB=" htslib "/lib/libhts.a")))
- (apply invoke "make" "CC=gcc" "CFLAGS=-Itabixpp" make-flags))))
+ (unpack "multichoose-src" "multichoose")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
- (lib (string-append (assoc-ref outputs "out") "/lib")))
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib")))
(for-each (lambda (file)
(install-file file bin))
(find-files "bin" ".*"))
- ;; The header files in src/ do not interface libvcflib,
- ;; therefore they are left out.
- (install-file "libvcflib.a" lib))
+ (install-file "libvcflib.so" lib)
+ (install-file "libvcflib.a" lib)
+ (for-each
+ (lambda (file)
+ (install-file file (string-append out "/include")))
+ (find-files "include" "\\.h(pp)?$"))
+ (mkdir-p (string-append lib "/pkgconfig"))
+ (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc")
+ (lambda _
+ (format #t "prefix=~a~@
+ exec_prefix=${prefix}~@
+ libdir=${exec_prefix}/lib~@
+ includedir=${prefix}/include~@
+ ~@
+ ~@
+ Name: libvcflib~@
+ Version: ~a~@
+ Requires: smithwaterman, fastahack~@
+ Description: C++ library for parsing and manipulating VCF files~@
+ Libs: -L${libdir} -lvcflib~@
+ Cflags: -I${includedir}~%"
+ out ,version))))
#t)))))
(home-page "https://github.com/vcflib/vcflib/")
(synopsis "Library for parsing and manipulating VCF files")
HCoop / jackhill / guix / guix.git / blobdiff