From e0625728125a21b410368eaae68c6fdf2710e11c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 6 Mar 2021 16:01:24 +0100 Subject: gnu: seqan: Use HTTPS home page URI. * gnu/packages/bioinformatics.scm (seqan)[home-page]: Use HTTPS URI. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d21e14360..9fc5cf8ecc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6608,7 +6608,7 @@ writing files into the .sra format.") `(("source" ,source) ("tar" ,tar) ("xz" ,xz))) - (home-page "http://www.seqan.de") + (home-page "https://www.seqan.de") (synopsis "Library for nucleotide sequence analysis") (description "SeqAn is a C++ library of efficient algorithms and data structures for -- cgit v1.2.3 From ea8e89292c2d8ad91de5adbc319d3d66545fb59c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 6 Mar 2021 16:05:44 +0100 Subject: gnu: seqan-1: Use HTTPS source URI. * gnu/packages/bioinformatics.scm (seqan-1)[source]: Use HTTPS URI. --- gnu/packages/bioinformatics.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9fc5cf8ecc..be07bd18a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6624,7 +6624,7 @@ bioinformatics file formats, sequence alignment, and more.") (version "1.4.2") (source (origin (method url-fetch) - (uri (string-append "http://packages.seqan.de/seqan-library/" + (uri (string-append "https://packages.seqan.de/seqan-library/" "seqan-library-" version ".tar.bz2")) (sha256 (base32 -- cgit v1.2.3 From 49d85b3f11a2ea28ac862857e7f040ef26ce39ae Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 9 Mar 2021 11:53:58 +0100 Subject: gnu: bbmap: Update to 38.90. * gnu/packages/bioinformatics.scm (bbmap): Update to 38.90. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index be07bd18a3..61c9e06a99 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14449,14 +14449,14 @@ is a Cython wrapper for FIt-SNE.") (define-public bbmap (package (name "bbmap") - (version "35.82") + (version "38.90") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bbmap/BBMap_" version ".tar.gz")) (sha256 (base32 - "1q4rfhxcb6z3gm8zg2davjz98w22lkf4hm9ikxz9kdl93pil3wkd")))) + "1wb94bcc006qq86x77z2rz0lc8m9f1kpnw6gdhjfg9bdaqf56rm3")))) (build-system ant-build-system) (arguments `(#:build-target "dist" -- cgit v1.2.3 From 133a91892315da653ec9654580942970b8e273be Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 9 Mar 2021 11:54:09 +0100 Subject: gnu: trim-galore: Update to 0.6.6. * gnu/packages/bioinformatics.scm (trim-galore): Update to 0.6.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 61c9e06a99..8b38c7ce0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11028,7 +11028,7 @@ with narrow binding events such as transcription factor ChIP-seq.") (define-public trim-galore (package (name "trim-galore") - (version "0.6.1") + (version "0.6.6") (source (origin (method git-fetch) @@ -11038,7 +11038,7 @@ with narrow binding events such as transcription factor ChIP-seq.") (file-name (git-file-name name version)) (sha256 (base32 - "1y31wbxwkm9xqzr5zv1pk5q418whnmlmgmfyxxpnl12h83m2i9iv")))) + "0yrwg6325j4sb9vnplvl3jplzab0qdhp92wl480qjinpfq88j4rs")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests -- cgit v1.2.3 From 5ae7414860eb6a6bd93ed30e962b257627d79ec9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 11 Mar 2021 16:53:45 +0200 Subject: gnu: Add bandage. * gnu/packages/bioinformatics.scm (bandage): New variable. --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8b38c7ce0d..b258b796f7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -52,6 +52,7 @@ #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module (guix build-system r) #:use-module (guix build-system ruby) #:use-module (guix build-system scons) @@ -125,6 +126,7 @@ #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) + #:use-module (gnu packages qt) #:use-module (gnu packages rdf) #:use-module (gnu packages readline) #:use-module (gnu packages ruby) @@ -13187,6 +13189,64 @@ concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.") (license license:expat))) +(define-public bandage + (package + (name "bandage") + (version "0.8.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rrwick/Bandage") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bbsn5f5x8wlspg4pbibqz6m5vin8c19nl224f3z3km0pkc97rwv")))) + (build-system qt-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'configure + (lambda _ + (invoke "qmake" "Bandage.pro"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (substitute* "tests/bandage_command_line_tests.sh" + (("^bandagepath=.*") + (string-append "bandagepath=" (getcwd) "/Bandage\n"))) + (with-directory-excursion "tests" + (setenv "XDG_RUNTIME_DIR" (getcwd)) + (invoke "./bandage_command_line_tests.sh"))) + #t)) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (install-file "Bandage" (string-append out "/bin")) + #t)))))) + (inputs + `(("qtbase" ,qtbase) + ("qtsvg" ,qtsvg))) + (native-inputs + `(("imagemagick" ,imagemagick))) + (home-page "https://rrwick.github.io/Bandage/") + (synopsis + "Bioinformatics Application for Navigating De novo Assembly Graphs Easily") + (description "Bandage is a program for visualising de novo assembly graphs. +It allows users to interact with the assembly graphs made by de novo assemblers +such as Velvet, SPAdes, MEGAHIT and others. De novo assembly graphs contain not +only assembled contigs but also the connections between those contigs, which +were previously not easily accessible. Bandage visualises assembly graphs, with +connections, using graph layout algorithms. Nodes in the drawn graph, which +represent contigs, can be automatically labelled with their ID, length or depth. +Users can interact with the graph by moving, labelling and colouring nodes. +Sequence information can also be extracted directly from the graph viewer. By +displaying connections between contigs, Bandage opens up new possibilities for +analysing and improving de novo assemblies that are not possible by looking at +contigs alone.") + (license (list license:gpl2+ ; bundled ogdf + license:gpl3+)))) + (define-public r-circus (package (name "r-circus") -- cgit v1.2.3 From a35ea5fed953df46cb33e517487e0eac528ec027 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:57:54 +0100 Subject: gnu: r-genefilter: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genefilter): Move from here... * gnu/packages/bioconductor.scm (r-genefilter): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ae8bae4bd9..f6f7766b49 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,34 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-genefilter + (package + (name "r-genefilter") + (version "1.72.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "genefilter" version)) + (sha256 + (base32 + "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) + (build-system r-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ("r-knitr" ,r-knitr))) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-survival" ,r-survival))) + (home-page "https://bioconductor.org/packages/genefilter") + (synopsis "Filter genes from high-throughput experiments") + (description + "This package provides basic functions for filtering genes from +high-throughput sequencing experiments.") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b258b796f7..557961b664 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,34 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-genefilter - (package - (name "r-genefilter") - (version "1.72.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "genefilter" version)) - (sha256 - (base32 - "1c6h3qnjvphs977qhv5vafvsb108r0q7xhaayly6qv6adqfn94rn")))) - (build-system r-build-system) - (native-inputs - `(("gfortran" ,gfortran) - ("r-knitr" ,r-knitr))) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-survival" ,r-survival))) - (home-page "https://bioconductor.org/packages/genefilter") - (synopsis "Filter genes from high-throughput experiments") - (description - "This package provides basic functions for filtering genes from -high-throughput sequencing experiments.") - (license license:artistic2.0))) - (define-public r-deseq2 (package (name "r-deseq2") -- cgit v1.2.3 From 373545855dd8434add9523d3cd51be66d60e8503 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:57:55 +0100 Subject: gnu: r-deseq2: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-deseq2): Move from here... * gnu/packages/bioconductor.scm (r-deseq2): ...to here. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 -------------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f6f7766b49..685ce10d6a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,44 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-deseq2 + (package + (name "r-deseq2") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DESeq2" version)) + (sha256 + (base32 + "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) + (properties `((upstream-name . "DESeq2"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-iranges" ,r-iranges) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo) + ("r-s4vectors" ,r-s4vectors) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DESeq2") + (synopsis "Differential gene expression analysis") + (description + "This package provides functions to estimate variance-mean dependence in +count data from high-throughput nucleotide sequencing assays and test for +differential expression based on a model using the negative binomial +distribution.") + (license license:lgpl3+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 557961b664..8f3e3f996b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,44 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-deseq2 - (package - (name "r-deseq2") - (version "1.30.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DESeq2" version)) - (sha256 - (base32 - "0q2f9cywrcmp1p7ii8f45g4dk4hsnjflq3yqhsxgnpv9fw338qpp")))) - (properties `((upstream-name . "DESeq2"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-iranges" ,r-iranges) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-rcpparmadillo" ,r-rcpparmadillo) - ("r-s4vectors" ,r-s4vectors) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DESeq2") - (synopsis "Differential gene expression analysis") - (description - "This package provides functions to estimate variance-mean dependence in -count data from high-throughput nucleotide sequencing assays and test for -differential expression based on a model using the negative binomial -distribution.") - (license license:lgpl3+))) - (define-public r-dexseq (package (name "r-dexseq") -- cgit v1.2.3 From d769b10714ba4ab96a27933b6840265cf6e06f37 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:57:56 +0100 Subject: gnu: r-dexseq: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-dexseq): Move from here... * gnu/packages/bioconductor.scm (r-dexseq): ...to here. --- gnu/packages/bioconductor.scm | 45 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 45 ----------------------------------------- 2 files changed, 45 insertions(+), 45 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 685ce10d6a..0c36b01545 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1525,6 +1525,51 @@ differential expression based on a model using the negative binomial distribution.") (license license:lgpl3+))) +(define-public r-dexseq + (package + (name "r-dexseq") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "DEXSeq" version)) + (sha256 + (base32 + "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) + (properties `((upstream-name . "DEXSeq"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biomart" ,r-biomart) + ("r-deseq2" ,r-deseq2) + ("r-genefilter" ,r-genefilter) + ("r-geneplotter" ,r-geneplotter) + ("r-genomicranges" ,r-genomicranges) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-statmod" ,r-statmod) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DEXSeq") + (synopsis "Inference of differential exon usage in RNA-Seq") + (description + "This package is focused on finding differential exon usage using RNA-seq +exon counts between samples with different experimental designs. It provides +functions that allows the user to make the necessary statistical tests based +on a model that uses the negative binomial distribution to estimate the +variance between biological replicates and generalized linear models for +testing. The package also provides functions for the visualization and +exploration of the results.") + (license license:gpl3+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8f3e3f996b..41372879fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,51 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-dexseq - (package - (name "r-dexseq") - (version "1.36.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "DEXSeq" version)) - (sha256 - (base32 - "0wfjb42xcr4wjy8a654b74411dky8hp6sp8xdwf0sxqgsxy106qi")))) - (properties `((upstream-name . "DEXSeq"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biomart" ,r-biomart) - ("r-deseq2" ,r-deseq2) - ("r-genefilter" ,r-genefilter) - ("r-geneplotter" ,r-geneplotter) - ("r-genomicranges" ,r-genomicranges) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-rcolorbrewer" ,r-rcolorbrewer) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-statmod" ,r-statmod) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DEXSeq") - (synopsis "Inference of differential exon usage in RNA-Seq") - (description - "This package is focused on finding differential exon usage using RNA-seq -exon counts between samples with different experimental designs. It provides -functions that allows the user to make the necessary statistical tests based -on a model that uses the negative binomial distribution to estimate the -variance between biological replicates and generalized linear models for -testing. The package also provides functions for the visualization and -exploration of the results.") - (license license:gpl3+))) - (define-public r-annotationforge (package (name "r-annotationforge") -- cgit v1.2.3 From ff92c2873c0c8ab9fa6e90020d656aac47dfb088 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:57:57 +0100 Subject: gnu: r-annotationforge: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-annotationforge): Move from here... * gnu/packages/bioconductor.scm (r-annotationforge): ...to here. --- gnu/packages/bioconductor.scm | 32 ++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 32 -------------------------------- 2 files changed, 32 insertions(+), 32 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0c36b01545..c698178067 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1487,6 +1487,38 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-annotationforge + (package + (name "r-annotationforge") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationForge" version)) + (sha256 + (base32 + "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) + (properties + `((upstream-name . "AnnotationForge"))) + (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-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationForge") + (synopsis "Code for building annotation database packages") + (description + "This package provides code for generating Annotation packages and their +databases. Packages produced are intended to be used with AnnotationDbi.") + (license license:artistic2.0))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 41372879fe..575158577c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,38 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-annotationforge - (package - (name "r-annotationforge") - (version "1.32.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationForge" version)) - (sha256 - (base32 - "0y3820dkvwz09wlmz9drx6gqpsr9cwppaiz40zafwfxbz65y8px7")))) - (properties - `((upstream-name . "AnnotationForge"))) - (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-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationForge") - (synopsis "Code for building annotation database packages") - (description - "This package provides code for generating Annotation packages and their -databases. Packages produced are intended to be used with AnnotationDbi.") - (license license:artistic2.0))) - (define-public r-rbgl (package (name "r-rbgl") -- cgit v1.2.3 From f44079bc2151979cde33704fec73f1da1726a2f5 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:57:58 +0100 Subject: gnu: r-rbgl: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rbgl): Move from here... * gnu/packages/bioconductor.scm (r-rbgl): ...to here. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 23 insertions(+), 23 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c698178067..1c298d61cf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1650,6 +1650,29 @@ high-throughput sequencing experiments.") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-rbgl + (package + (name "r-rbgl") + (version "1.66.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RBGL" version)) + (sha256 + (base32 + "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) + (properties `((upstream-name . "RBGL"))) + (build-system r-build-system) + (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 + "This package provides a fairly extensive and comprehensive interface to +the graph algorithms contained in the Boost library.") + (license license:artistic2.0))) + (define-public r-regioner (package (name "r-regioner") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 575158577c..788f780f8d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,29 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-rbgl - (package - (name "r-rbgl") - (version "1.66.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "RBGL" version)) - (sha256 - (base32 - "016vyzgixb3gjpzi21rbs6ngnnqcxr77krwjjf1ldnzzj8vqrqsz")))) - (properties `((upstream-name . "RBGL"))) - (build-system r-build-system) - (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 - "This package provides a fairly extensive and comprehensive interface to -the graph algorithms contained in the Boost library.") - (license license:artistic2.0))) - (define-public r-gseabase (package (name "r-gseabase") -- cgit v1.2.3 From 031fdda47af642d4316e128f9ca0c3fe2cf8b4bb Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:57:59 +0100 Subject: gnu: r-gseabase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-gseabase): Move from here... * gnu/packages/bioconductor.scm (r-gseabase): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1c298d61cf..a89797adc8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1630,6 +1630,35 @@ exploration of the results.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-gseabase + (package + (name "r-gseabase") + (version "1.52.1") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GSEABase" version)) + (sha256 + (base32 + "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) + (properties `((upstream-name . "GSEABase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-graph" ,r-graph) + ("r-xml" ,r-xml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GSEABase") + (synopsis "Gene set enrichment data structures and methods") + (description + "This package provides classes and methods to support @dfn{Gene Set +Enrichment Analysis} (GSEA).") + (license license:artistic2.0))) + (define-public r-hpar (package (name "r-hpar") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 788f780f8d..4daaacd0cc 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,35 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-gseabase - (package - (name "r-gseabase") - (version "1.52.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GSEABase" version)) - (sha256 - (base32 - "0dawh1kjmf6921jm77j2s2phrq5237pjc4sdh8fkln89gf48zx6i")))) - (properties `((upstream-name . "GSEABase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-graph" ,r-graph) - ("r-xml" ,r-xml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GSEABase") - (synopsis "Gene set enrichment data structures and methods") - (description - "This package provides classes and methods to support @dfn{Gene Set -Enrichment Analysis} (GSEA).") - (license license:artistic2.0))) - (define-public r-category (package (name "r-category") -- cgit v1.2.3 From 4e7cf96c9f12c31152f4c67a1ce4d7d2ad9b2461 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:58:00 +0100 Subject: gnu: r-category: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-category): Move from here... * gnu/packages/bioconductor.scm (r-category): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a89797adc8..aa172c5244 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1519,6 +1519,37 @@ microarrays.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-category + (package + (name "r-category") + (version "2.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Category" version)) + (sha256 + (base32 + "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) + (properties `((upstream-name . "Category"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-genefilter" ,r-genefilter) + ("r-graph" ,r-graph) + ("r-gseabase" ,r-gseabase) + ("r-matrix" ,r-matrix) + ("r-rbgl" ,r-rbgl) + ("r-dbi" ,r-dbi))) + (home-page "https://bioconductor.org/packages/Category") + (synopsis "Category analysis") + (description + "This package provides a collection of tools for performing category +analysis.") + (license license:artistic2.0))) + (define-public r-deseq2 (package (name "r-deseq2") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4daaacd0cc..ae3a8013f0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,37 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-category - (package - (name "r-category") - (version "2.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "Category" version)) - (sha256 - (base32 - "0m77wpnica0h2ia9ajdaiga4plgz1s9wls6pdnxzk7kwl8a68wkr")))) - (properties `((upstream-name . "Category"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-genefilter" ,r-genefilter) - ("r-graph" ,r-graph) - ("r-gseabase" ,r-gseabase) - ("r-matrix" ,r-matrix) - ("r-rbgl" ,r-rbgl) - ("r-dbi" ,r-dbi))) - (home-page "https://bioconductor.org/packages/Category") - (synopsis "Category analysis") - (description - "This package provides a collection of tools for performing category -analysis.") - (license license:artistic2.0))) - (define-public r-gostats (package (name "r-gostats") -- cgit v1.2.3 From 2a9705768808ff8b76bf38a7ae9445b2c756ba46 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:58:01 +0100 Subject: gnu: r-gostats: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-gostats): Move from here... * gnu/packages/bioconductor.scm (r-gostats): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index aa172c5244..a4618ec90a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1661,6 +1661,37 @@ exploration of the results.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-gostats + (package + (name "r-gostats") + (version "2.56.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "GOstats" version)) + (sha256 + (base32 + "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) + (properties `((upstream-name . "GOstats"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-annotationdbi" ,r-annotationdbi) + ("r-annotationforge" ,r-annotationforge) + ("r-biobase" ,r-biobase) + ("r-category" ,r-category) + ("r-go-db" ,r-go-db) + ("r-graph" ,r-graph) + ("r-rgraphviz" ,r-rgraphviz) + ("r-rbgl" ,r-rbgl))) + (home-page "https://bioconductor.org/packages/GOstats") + (synopsis "Tools for manipulating GO and microarrays") + (description + "This package provides a set of tools for interacting with GO and +microarray data. A variety of basic manipulation tools for graphs, hypothesis +testing and other simple calculations.") + (license license:artistic2.0))) + (define-public r-gseabase (package (name "r-gseabase") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ae3a8013f0..c4713fc5cf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,37 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-gostats - (package - (name "r-gostats") - (version "2.56.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "GOstats" version)) - (sha256 - (base32 - "18q8p0fv9fl2r6zjxknfjwqxr69dlyxy6c8amzn6c6dwjq1cxk6j")))) - (properties `((upstream-name . "GOstats"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-annotationdbi" ,r-annotationdbi) - ("r-annotationforge" ,r-annotationforge) - ("r-biobase" ,r-biobase) - ("r-category" ,r-category) - ("r-go-db" ,r-go-db) - ("r-graph" ,r-graph) - ("r-rgraphviz" ,r-rgraphviz) - ("r-rbgl" ,r-rbgl))) - (home-page "https://bioconductor.org/packages/GOstats") - (synopsis "Tools for manipulating GO and microarrays") - (description - "This package provides a set of tools for interacting with GO and -microarray data. A variety of basic manipulation tools for graphs, hypothesis -testing and other simple calculations.") - (license license:artistic2.0))) - (define-public r-shortread (package (name "r-shortread") -- cgit v1.2.3 From 8957efa8ef940685811b9e55eb7178ecd33abb40 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:58:02 +0100 Subject: gnu: r-shortread: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-shortread): Move from here... * gnu/packages/bioconductor.scm (r-shortread): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 ----------------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index a4618ec90a..283ae7adf8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1845,6 +1845,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-shortread + (package + (name "r-shortread") + (version "1.48.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ShortRead" version)) + (sha256 + (base32 + "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) + (properties `((upstream-name . "ShortRead"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-rhtslib" ,r-rhtslib) + ("r-hwriter" ,r-hwriter) + ("r-iranges" ,r-iranges) + ("r-lattice" ,r-lattice) + ("r-latticeextra" ,r-latticeextra) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (home-page "https://bioconductor.org/packages/ShortRead") + (synopsis "FASTQ input and manipulation tools") + (description + "This package implements sampling, iteration, and input of FASTQ files. +It includes functions for filtering and trimming reads, and for generating a +quality assessment report. Data are represented as +@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of +purposes. The package also contains legacy support for early single-end, +ungapped alignment formats.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c4713fc5cf..f363d64550 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,49 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-shortread - (package - (name "r-shortread") - (version "1.48.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "ShortRead" version)) - (sha256 - (base32 - "0w4m8d3h660mmr2ymp206r1n4aqssxmkv8yxkbr5y1swrahxzfk9")))) - (properties `((upstream-name . "ShortRead"))) - (build-system r-build-system) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-rhtslib" ,r-rhtslib) - ("r-hwriter" ,r-hwriter) - ("r-iranges" ,r-iranges) - ("r-lattice" ,r-lattice) - ("r-latticeextra" ,r-latticeextra) - ("r-rsamtools" ,r-rsamtools) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (home-page "https://bioconductor.org/packages/ShortRead") - (synopsis "FASTQ input and manipulation tools") - (description - "This package implements sampling, iteration, and input of FASTQ files. -It includes functions for filtering and trimming reads, and for generating a -quality assessment report. Data are represented as -@code{DNAStringSet}-derived objects, and easily manipulated for a diversity of -purposes. The package also contains legacy support for early single-end, -ungapped alignment formats.") - (license license:artistic2.0))) - (define-public r-systempiper (package (name "r-systempiper") -- cgit v1.2.3 From df6b3c25bbaabd5153c2472a5082c24934e16492 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 8 Mar 2021 18:58:28 +0100 Subject: gnu: r-systempiper: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-systempiper): Move from here... * gnu/packages/bioconductor.scm (r-systempiper): ...to here. --- gnu/packages/bioconductor.scm | 54 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 54 ----------------------------------------- 2 files changed, 54 insertions(+), 54 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 283ae7adf8..526c2eecbb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1888,6 +1888,60 @@ purposes. The package also contains legacy support for early single-end, ungapped alignment formats.") (license license:artistic2.0))) +(define-public r-systempiper + (package + (name "r-systempiper") + (version "1.24.3") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "systemPipeR" version)) + (sha256 + (base32 + "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) + (properties `((upstream-name . "systemPipeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotate" ,r-annotate) + ("r-assertthat" ,r-assertthat) + ("r-batchtools" ,r-batchtools) + ("r-biostrings" ,r-biostrings) + ("r-deseq2" ,r-deseq2) + ("r-dot" ,r-dot) + ("r-edger" ,r-edger) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-go-db" ,r-go-db) + ("r-gostats" ,r-gostats) + ("r-iranges" ,r-iranges) + ("r-limma" ,r-limma) + ("r-magrittr" ,r-magrittr) + ("r-pheatmap" ,r-pheatmap) + ("r-rjson" ,r-rjson) + ("r-rsamtools" ,r-rsamtools) + ("r-rsvg" ,r-rsvg) + ("r-shortread" ,r-shortread) + ("r-stringr" ,r-stringr) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-yaml" ,r-yaml) + ("r-variantannotation" ,r-variantannotation))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/tgirke/systemPipeR") + (synopsis "Next generation sequencing workflow and reporting environment") + (description + "This R package provides tools for building and running automated +end-to-end analysis workflows for a wide range of @dfn{next generation +sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. +Important features include a uniform workflow interface across different NGS +applications, automated report generation, and support for running both R and +command-line software, such as NGS aligners or peak/variant callers, on local +computers or compute clusters. Efficient handling of complex sample sets and +experimental designs is facilitated by a consistently implemented sample +annotation infrastructure.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f363d64550..b2d10457fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,60 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-systempiper - (package - (name "r-systempiper") - (version "1.24.3") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "systemPipeR" version)) - (sha256 - (base32 - "0ffazyl2q9plbhwlxi04s3fvnli6qj95n7bkjc21535bbi08xfki")))) - (properties `((upstream-name . "systemPipeR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotate" ,r-annotate) - ("r-assertthat" ,r-assertthat) - ("r-batchtools" ,r-batchtools) - ("r-biostrings" ,r-biostrings) - ("r-deseq2" ,r-deseq2) - ("r-dot" ,r-dot) - ("r-edger" ,r-edger) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-ggplot2" ,r-ggplot2) - ("r-go-db" ,r-go-db) - ("r-gostats" ,r-gostats) - ("r-iranges" ,r-iranges) - ("r-limma" ,r-limma) - ("r-magrittr" ,r-magrittr) - ("r-pheatmap" ,r-pheatmap) - ("r-rjson" ,r-rjson) - ("r-rsamtools" ,r-rsamtools) - ("r-rsvg" ,r-rsvg) - ("r-shortread" ,r-shortread) - ("r-stringr" ,r-stringr) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-yaml" ,r-yaml) - ("r-variantannotation" ,r-variantannotation))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://github.com/tgirke/systemPipeR") - (synopsis "Next generation sequencing workflow and reporting environment") - (description - "This R package provides tools for building and running automated -end-to-end analysis workflows for a wide range of @dfn{next generation -sequence} (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. -Important features include a uniform workflow interface across different NGS -applications, automated report generation, and support for running both R and -command-line software, such as NGS aligners or peak/variant callers, on local -computers or compute clusters. Efficient handling of complex sample sets and -experimental designs is facilitated by a consistently implemented sample -annotation infrastructure.") - (license license:artistic2.0))) - (define-public r-grohmm (package (name "r-grohmm") -- cgit v1.2.3 From ad34eb222c9ebc2b31f03b70ba6655ebe8ee74b5 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 15 Mar 2021 11:38:29 +0100 Subject: gnu: Add python-drep. * gnu/packages/bioinformatics.scm (python-drep): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b2d10457fe..c629b79c39 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13147,6 +13147,36 @@ create connections between analogous cells in different batches without altering the counts or PCA space.") (license license:expat))) +(define-public python-drep + (package + (name "python-drep") + (version "3.2.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "drep" version)) + (sha256 + (base32 + "08vk0x6v5c5n7afgd5pcjhsvb424absypxy22hw1cm1n9kirbi77")))) + (build-system python-build-system) + (propagated-inputs + `(("python-biopython" ,python-biopython) + ("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-pytest" ,python-pytest) + ("python-scikit-learn" ,python-scikit-learn) + ("python-seaborn" ,python-seaborn) + ("python-tqdm" ,python-tqdm))) + (home-page "https://github.com/MrOlm/drep") + (synopsis "De-replication of microbial genomes assembled from multiple samples") + (description + "dRep is a Python program for rapidly comparing large numbers of genomes. +dRep can also \"de-replicate\" a genome set by identifying groups of highly +similar genomes and choosing the best representative genome for each genome +set.") + (license license:expat))) + (define-public gffcompare (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41") (revision "1")) -- cgit v1.2.3 From 6e0ed09e687d9b8ae2cf2d01a9946b84bc8bf641 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 15 Mar 2021 11:38:40 +0100 Subject: gnu: Add instrain. * gnu/packages/bioinformatics.scm (instrain): New variable. --- gnu/packages/bioinformatics.scm | 53 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c629b79c39..b0736d32e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13177,6 +13177,59 @@ similar genomes and choosing the best representative genome for each genome set.") (license license:expat))) +(define-public instrain + (package + (name "instrain") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "inStrain" version)) + (sha256 + (base32 + "0ykqlpf6yz4caihsaz3ys00cyvlr7wdj4s9a8rh56q5r8xf80ic0")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-relative-imports + (lambda _ + (substitute* "docker/run_instrain.py" + (("from s3_utils") + "from .s3_utils") + (("from job_utils") + "from .job_utils"))))))) + (inputs + `(("python-biopython" ,python-biopython) + ("python-boto3" ,python-boto3) + ("python-h5py" ,python-h5py) + ("python-lmfit" ,python-lmfit) + ("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) + ("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-psutil" ,python-psutil) + ("python-pysam" ,python-pysam) + ("python-scikit-learn" ,python-scikit-learn) + ("python-seaborn" ,python-seaborn) + ("python-tqdm" ,python-tqdm) + ;; drep is needed for deprecated plot utilities + ("python-drep" ,python-drep))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/MrOlm/inStrain") + (synopsis "Calculation of strain-level metrics") + (description + "inStrain is a Python program for analysis of co-occurring genome +populations from metagenomes that allows highly accurate genome comparisons, +analysis of coverage, microdiversity, and linkage, and sensitive SNP detection +with gene localization and synonymous non-synonymous identification.") + ;; The tool itself says that the license is "MIT", but the repository + ;; contains a LICENSE file with the GPLv3. + ;; See https://github.com/MrOlm/inStrain/issues/51 + (license license:expat))) + (define-public gffcompare (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41") (revision "1")) -- cgit v1.2.3 From 134404b437a2b17bbe072b263884f6ff5d8daf86 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:27 +0100 Subject: gnu: r-biocviews: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biocviews): Move from here... * gnu/packages/bioconductor.scm (r-biocviews): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 4f8e0562b1..c02d1c7877 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8477,6 +8477,34 @@ monograph.") different graph related packages produced by Bioconductor.") (license license:artistic2.0))) +(define-public r-biocviews + (package + (name "r-biocviews") + (version "1.58.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biocViews" version)) + (sha256 + (base32 + "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) + (properties + `((upstream-name . "biocViews"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocmanager" ,r-biocmanager) + ("r-graph" ,r-graph) + ("r-rbgl" ,r-rbgl) + ("r-rcurl" ,r-rcurl) + ("r-xml" ,r-xml) + ("r-runit" ,r-runit))) + (home-page "https://bioconductor.org/packages/biocViews") + (synopsis "Bioconductor package categorization helper") + (description "The purpose of biocViews is to create HTML pages that +categorize packages in a Bioconductor package repository according to keywords, +also known as views, in a controlled vocabulary.") + (license license:artistic2.0))) + (define-public r-experimenthub (package (name "r-experimenthub") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b0736d32e4..8169ff4f26 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7718,34 +7718,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biocviews - (package - (name "r-biocviews") - (version "1.58.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biocViews" version)) - (sha256 - (base32 - "1by2639z7n62z84dr8rj9jz12gsd1k8q42zsnxacxbwfwp6h0cl4")))) - (properties - `((upstream-name . "biocViews"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocmanager" ,r-biocmanager) - ("r-graph" ,r-graph) - ("r-rbgl" ,r-rbgl) - ("r-rcurl" ,r-rcurl) - ("r-xml" ,r-xml) - ("r-runit" ,r-runit))) - (home-page "https://bioconductor.org/packages/biocViews") - (synopsis "Bioconductor package categorization helper") - (description "The purpose of biocViews is to create HTML pages that -categorize packages in a Bioconductor package repository according to keywords, -also known as views, in a controlled vocabulary.") - (license license:artistic2.0))) - (define-public r-biocstyle (package (name "r-biocstyle") -- cgit v1.2.3 From 5ac55aea8b78439cc72b70718cb7922599182712 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:28 +0100 Subject: gnu: r-biocstyle: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biocstyle): Move from here... * gnu/packages/bioconductor.scm (r-biocstyle): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c02d1c7877..ca9bcc07eb 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8477,6 +8477,34 @@ monograph.") different graph related packages produced by Bioconductor.") (license license:artistic2.0))) +(define-public r-biocstyle + (package + (name "r-biocstyle") + (version "2.18.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocStyle" version)) + (sha256 + (base32 + "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) + (properties + `((upstream-name . "BiocStyle"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocmanager" ,r-biocmanager) + ("r-bookdown" ,r-bookdown) + ("r-knitr" ,r-knitr) + ("r-rmarkdown" ,r-rmarkdown) + ("r-yaml" ,r-yaml))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocStyle") + (synopsis "Bioconductor formatting styles") + (description "This package provides standard formatting styles for +Bioconductor PDF and HTML documents. Package vignettes illustrate use and +functionality.") + (license license:artistic2.0))) + (define-public r-biocviews (package (name "r-biocviews") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8169ff4f26..c90dcada7b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7718,34 +7718,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biocstyle - (package - (name "r-biocstyle") - (version "2.18.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocStyle" version)) - (sha256 - (base32 - "0rsxyna4dd99x42vc82mlkxx774vb9375llpakg53max1hhwkrqp")))) - (properties - `((upstream-name . "BiocStyle"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocmanager" ,r-biocmanager) - ("r-bookdown" ,r-bookdown) - ("r-knitr" ,r-knitr) - ("r-rmarkdown" ,r-rmarkdown) - ("r-yaml" ,r-yaml))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocStyle") - (synopsis "Bioconductor formatting styles") - (description "This package provides standard formatting styles for -Bioconductor PDF and HTML documents. Package vignettes illustrate use and -functionality.") - (license license:artistic2.0))) - (define-public r-bioccheck (package (name "r-bioccheck") -- cgit v1.2.3 From d5576b6eb7808574dd519bf7591b4cf08ea6cb2c Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:26 +0100 Subject: gnu: r-grohmm: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-grohmm): Move from here... * gnu/packages/bioconductor.scm (r-grohmm): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ca9bcc07eb..91d02639a3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8567,6 +8567,33 @@ and manages a local cache of files retrieved enabling quick and reproducible access.") (license license:artistic2.0))) +(define-public r-grohmm + (package + (name "r-grohmm") + (version "1.24.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "groHMM" version)) + (sha256 + (base32 + "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) + (properties `((upstream-name . "groHMM"))) + (build-system r-build-system) + (propagated-inputs + `(("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicalignments" ,r-genomicalignments) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-mass" ,r-mass) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://github.com/Kraus-Lab/groHMM") + (synopsis "GRO-seq analysis pipeline") + (description + "This package provides a pipeline for the analysis of GRO-seq data.") + (license license:gpl3+))) + (define-public r-multiassayexperiment (package (name "r-multiassayexperiment") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c90dcada7b..ad3ae204e1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7387,33 +7387,6 @@ includes software to ") (license license:cc0)))) -(define-public r-grohmm - (package - (name "r-grohmm") - (version "1.24.0") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "groHMM" version)) - (sha256 - (base32 - "08pap9wsaxl4jjlc1py0rc019gmi6daa0f9cr3ih1d97wybncanx")))) - (properties `((upstream-name . "groHMM"))) - (build-system r-build-system) - (propagated-inputs - `(("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicalignments" ,r-genomicalignments) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-mass" ,r-mass) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://github.com/Kraus-Lab/groHMM") - (synopsis "GRO-seq analysis pipeline") - (description - "This package provides a pipeline for the analysis of GRO-seq data.") - (license license:gpl3+))) - (define-public vsearch (package (name "vsearch") -- cgit v1.2.3 From 852fa82d4ccd902dfd7b8e673d4d1f71fd69e89a Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:29 +0100 Subject: gnu: r-bioccheck: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-bioccheck): Move from here... * gnu/packages/bioconductor.scm (r-bioccheck): ...to here. --- gnu/packages/bioconductor.scm | 49 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 49 ----------------------------------------- 2 files changed, 49 insertions(+), 49 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 91d02639a3..7c97e52312 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -8452,6 +8452,55 @@ microarray data.") monograph.") (license license:artistic2.0))) +(define-public r-bioccheck + (package + (name "r-bioccheck") + (version "1.26.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocCheck" version)) + (sha256 + (base32 + "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) + (properties + `((upstream-name . "BiocCheck"))) + (build-system r-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + ;; This package can be used by calling BiocCheck() from + ;; within R, or by running R CMD BiocCheck . This phase + ;; makes sure the latter works. For this to work, the BiocCheck + ;; script must be somewhere on the PATH (not the R bin directory). + (add-after 'install 'install-bioccheck-subcommand + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (dest-dir (string-append out "/bin")) + (script-dir + (string-append out "/site-library/BiocCheck/script/"))) + (mkdir-p dest-dir) + (symlink (string-append script-dir "/checkBadDeps.R") + (string-append dest-dir "/checkBadDeps.R")) + (symlink (string-append script-dir "/BiocCheck") + (string-append dest-dir "/BiocCheck"))) + #t))))) + (propagated-inputs + `(("r-codetools" ,r-codetools) + ("r-graph" ,r-graph) + ("r-httr" ,r-httr) + ("r-knitr" ,r-knitr) + ("r-optparse" ,r-optparse) + ("r-biocmanager" ,r-biocmanager) + ("r-biocviews" ,r-biocviews) + ("r-stringdist" ,r-stringdist))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocCheck") + (synopsis "Executes Bioconductor-specific package checks") + (description "This package contains tools to perform additional quality +checks on R packages that are to be submitted to the Bioconductor repository.") + (license license:artistic2.0))) + (define-public r-biocgraph (package (name "r-biocgraph") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ad3ae204e1..d8d64818d2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,55 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-bioccheck - (package - (name "r-bioccheck") - (version "1.26.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocCheck" version)) - (sha256 - (base32 - "1hyncn9zqj432da95k86rm5b28nbwrvzm52jbhisifkxj1j43cib")))) - (properties - `((upstream-name . "BiocCheck"))) - (build-system r-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - ;; This package can be used by calling BiocCheck() from - ;; within R, or by running R CMD BiocCheck . This phase - ;; makes sure the latter works. For this to work, the BiocCheck - ;; script must be somewhere on the PATH (not the R bin directory). - (add-after 'install 'install-bioccheck-subcommand - (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (dest-dir (string-append out "/bin")) - (script-dir - (string-append out "/site-library/BiocCheck/script/"))) - (mkdir-p dest-dir) - (symlink (string-append script-dir "/checkBadDeps.R") - (string-append dest-dir "/checkBadDeps.R")) - (symlink (string-append script-dir "/BiocCheck") - (string-append dest-dir "/BiocCheck"))) - #t))))) - (propagated-inputs - `(("r-codetools" ,r-codetools) - ("r-graph" ,r-graph) - ("r-httr" ,r-httr) - ("r-knitr" ,r-knitr) - ("r-optparse" ,r-optparse) - ("r-biocmanager" ,r-biocmanager) - ("r-biocviews" ,r-biocviews) - ("r-stringdist" ,r-stringdist))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocCheck") - (synopsis "Executes Bioconductor-specific package checks") - (description "This package contains tools to perform additional quality -checks on R packages that are to be submitted to the Bioconductor repository.") - (license license:artistic2.0))) - (define-public r-s4vectors (package (name "r-s4vectors") -- cgit v1.2.3 From d64e3a487ba890b1aa6b24b7be917f55f80740a8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:30 +0100 Subject: gnu: r-s4vectors: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-s4vectors): Move from here... * gnu/packages/bioconductor.scm (r-s4vectors): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 28 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7c97e52312..ed34a9308a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen +;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -9154,6 +9155,33 @@ generated.") routines.") (license license:lgpl2.0+))) +(define-public r-s4vectors + (package + (name "r-s4vectors") + (version "0.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "S4Vectors" version)) + (sha256 + (base32 + "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) + (properties + `((upstream-name . "S4Vectors"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/S4Vectors") + (synopsis "S4 implementation of vectors and lists") + (description + "The S4Vectors package defines the @code{Vector} and @code{List} virtual +classes and a set of generic functions that extend the semantic of ordinary +vectors and lists in R. Package developers can easily implement vector-like +or list-like objects as concrete subclasses of @code{Vector} or @code{List}. +In addition, a few low-level concrete subclasses of general interest (e.g. +@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the +S4Vectors package itself.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on preprocessorcore, which is a ;; Bioconductor package. (define-public r-wgcna diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d8d64818d2..1fcb436f0d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,33 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-s4vectors - (package - (name "r-s4vectors") - (version "0.28.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "S4Vectors" version)) - (sha256 - (base32 - "0fhf4lsfxrim7glazh6ng46ykzaly5ggwpg170vcz4cc24prv0rh")))) - (properties - `((upstream-name . "S4Vectors"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/S4Vectors") - (synopsis "S4 implementation of vectors and lists") - (description - "The S4Vectors package defines the @code{Vector} and @code{List} virtual -classes and a set of generic functions that extend the semantic of ordinary -vectors and lists in R. Package developers can easily implement vector-like -or list-like objects as concrete subclasses of @code{Vector} or @code{List}. -In addition, a few low-level concrete subclasses of general interest (e.g. -@code{DataFrame}, @code{Rle}, and @code{Hits}) are implemented in the -S4Vectors package itself.") - (license license:artistic2.0))) - (define-public r-iranges (package (name "r-iranges") -- cgit v1.2.3 From 9949f459bff3980f59db8925a90891577e4f91d6 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:31 +0100 Subject: gnu: r-iranges: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-iranges): Move from here... * gnu/packages/bioconductor.scm (r-iranges): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 30 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ed34a9308a..68c5ed7768 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2,6 +2,7 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins +;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -1244,6 +1245,35 @@ and evaluate clustering results.") arbitrary genomic intervals along chromosomal ideogram.") (license license:gpl2))) +(define-public r-iranges + (package + (name "r-iranges") + (version "2.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "IRanges" version)) + (sha256 + (base32 + "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) + (properties + `((upstream-name . "IRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/IRanges") + (synopsis "Infrastructure for manipulating intervals on sequences") + (description + "This package provides efficient low-level and highly reusable S4 classes +for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more +generally, data that can be organized sequentially (formally defined as +@code{Vector} objects), as well as views on these @code{Vector} objects. +Efficient list-like classes are also provided for storing big collections of +instances of the basic classes. All classes in the package use consistent +naming and share the same rich and consistent \"Vector API\" as much as +possible.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 ;; from Bioconductor. (define-public r-deconstructsigs diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1fcb436f0d..36ecf47467 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,35 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-iranges - (package - (name "r-iranges") - (version "2.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "IRanges" version)) - (sha256 - (base32 - "01mx46a82vd3gz705pj0kk4wpxg683s8jqxchzjia3gz00b4qw52")))) - (properties - `((upstream-name . "IRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/IRanges") - (synopsis "Infrastructure for manipulating intervals on sequences") - (description - "This package provides efficient low-level and highly reusable S4 classes -for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more -generally, data that can be organized sequentially (formally defined as -@code{Vector} objects), as well as views on these @code{Vector} objects. -Efficient list-like classes are also provided for storing big collections of -instances of the basic classes. All classes in the package use consistent -naming and share the same rich and consistent \"Vector API\" as much as -possible.") - (license license:artistic2.0))) - (define-public r-genomeinfodbdata (package (name "r-genomeinfodbdata") -- cgit v1.2.3 From 8d6d75ff392af1d2633a2ffc07f29c5c1da0071c Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:32 +0100 Subject: gnu: r-genomeinfodbdata: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodbdata): ...to here. [source]: Use 'bioconductor-uri'. --- gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++ gnu/packages/bioinformatics.scm | 23 ----------------------- 2 files changed, 20 insertions(+), 23 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 68c5ed7768..53f025ec61 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3,6 +3,7 @@ ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen ;;; Copyright © 2016 Pjotr Prins ;;; Copyright © 2016 Ben Woodcroft +;;; Copyright © 2017 Efraim Flashner ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2020, 2021 Simon Tournier ;;; Copyright © 2020 Peter Lo @@ -391,6 +392,25 @@ musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-genomeinfodbdata + (package + (name "r-genomeinfodbdata") + (version "1.2.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDbData" version 'annotation)) + (sha256 + (base32 + "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) + (properties + `((upstream-name . "GenomeInfoDbData"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/GenomeInfoDbData") + (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") + (description "This package contains data for mapping between NCBI taxonomy +ID and species. It is used by functions in the GenomeInfoDb package.") + (license license:artistic2.0))) + (define-public r-homo-sapiens (package (name "r-homo-sapiens") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 36ecf47467..25ade2b9db 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,29 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomeinfodbdata - (package - (name "r-genomeinfodbdata") - (version "1.2.0") - (source (origin - (method url-fetch) - ;; We cannot use bioconductor-uri here because this tarball is - ;; located under "data/annotation/" instead of "bioc/". - (uri (string-append "https://bioconductor.org/packages/release/" - "data/annotation/src/contrib/GenomeInfoDbData_" - version ".tar.gz")) - (sha256 - (base32 - "0di6nlqpsyqf693k2na65ayqldih563x3zfrczpqc5q2hl5kg35c")))) - (properties - `((upstream-name . "GenomeInfoDbData"))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/GenomeInfoDbData") - (synopsis "Species and taxonomy ID look up tables for GenomeInfoDb") - (description "This package contains data for mapping between NCBI taxonomy -ID and species. It is used by functions in the GenomeInfoDb package.") - (license license:artistic2.0))) - (define-public r-genomeinfodb (package (name "r-genomeinfodb") -- cgit v1.2.3 From 35b62c044e45a3add35b62839b07030f704bf708 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:33 +0100 Subject: gnu: r-genomeinfodb: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomeinfodb): Move from here... * gnu/packages/bioconductor.scm (r-genomeinfodb): ...to here. --- gnu/packages/bioconductor.scm | 30 ++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 30 ------------------------------ 2 files changed, 30 insertions(+), 30 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 53f025ec61..b4456d13c8 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1712,6 +1712,36 @@ exploration of the results.") high-throughput sequencing experiments.") (license license:artistic2.0))) +(define-public r-genomeinfodb + (package + (name "r-genomeinfodb") + (version "1.26.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomeInfoDb" version)) + (sha256 + (base32 + "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v")))) + (properties + `((upstream-name . "GenomeInfoDb"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodbdata" ,r-genomeinfodbdata) + ("r-iranges" ,r-iranges) + ("r-rcurl" ,r-rcurl) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomeInfoDb") + (synopsis "Utilities for manipulating chromosome identifiers") + (description + "This package contains data and functions that define and allow +translation between different chromosome sequence naming conventions (e.g., +\"chr1\" versus \"1\"), including a function that attempts to place sequence +names in their natural, rather than lexicographic, order.") + (license license:artistic2.0))) + (define-public r-gostats (package (name "r-gostats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 25ade2b9db..ff6996011e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,36 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomeinfodb - (package - (name "r-genomeinfodb") - (version "1.26.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomeInfoDb" version)) - (sha256 - (base32 - "092izc49maxjhf6m4b0qx21ad16dz7bmxy5pysp3vkyhdrfa2f7v")))) - (properties - `((upstream-name . "GenomeInfoDb"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodbdata" ,r-genomeinfodbdata) - ("r-iranges" ,r-iranges) - ("r-rcurl" ,r-rcurl) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomeInfoDb") - (synopsis "Utilities for manipulating chromosome identifiers") - (description - "This package contains data and functions that define and allow -translation between different chromosome sequence naming conventions (e.g., -\"chr1\" versus \"1\"), including a function that attempts to place sequence -names in their natural, rather than lexicographic, order.") - (license license:artistic2.0))) - (define-public r-edger (package (name "r-edger") -- cgit v1.2.3 From 082f3c54337aaba40b978dfa9963f8ed6f20123d Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:34 +0100 Subject: gnu: r-edger: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-edger): Move from here... * gnu/packages/bioconductor.scm (r-edger): ...to here. --- gnu/packages/bioconductor.scm | 28 ++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 28 ---------------------------- 2 files changed, 28 insertions(+), 28 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b4456d13c8..fb0127b7ca 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1684,6 +1684,34 @@ testing. The package also provides functions for the visualization and exploration of the results.") (license license:gpl3+))) +(define-public r-edger + (package + (name "r-edger") + (version "3.32.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "edgeR" version)) + (sha256 + (base32 + "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) + (properties `((upstream-name . "edgeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-limma" ,r-limma) + ("r-locfit" ,r-locfit) + ("r-rcpp" ,r-rcpp) + ("r-statmod" ,r-statmod))) ;for estimateDisp + (home-page "http://bioinf.wehi.edu.au/edgeR") + (synopsis "EdgeR does empirical analysis of digital gene expression data") + (description "This package can do differential expression analysis of +RNA-seq expression profiles with biological replication. It implements a range +of statistical methodology based on the negative binomial distributions, +including empirical Bayes estimation, exact tests, generalized linear models +and quasi-likelihood tests. It be applied to differential signal analysis of +other types of genomic data that produce counts, including ChIP-seq, SAGE and +CAGE.") + (license license:gpl2+))) + (define-public r-genefilter (package (name "r-genefilter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ff6996011e..dc0d7a2906 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,34 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-edger - (package - (name "r-edger") - (version "3.32.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "edgeR" version)) - (sha256 - (base32 - "1gaic8qf6a6sy0bmydh1xzf52w0wnq31aanpvw3a30pfsi218bcp")))) - (properties `((upstream-name . "edgeR"))) - (build-system r-build-system) - (propagated-inputs - `(("r-limma" ,r-limma) - ("r-locfit" ,r-locfit) - ("r-rcpp" ,r-rcpp) - ("r-statmod" ,r-statmod))) ;for estimateDisp - (home-page "http://bioinf.wehi.edu.au/edgeR") - (synopsis "EdgeR does empirical analysis of digital gene expression data") - (description "This package can do differential expression analysis of -RNA-seq expression profiles with biological replication. It implements a range -of statistical methodology based on the negative binomial distributions, -including empirical Bayes estimation, exact tests, generalized linear models -and quasi-likelihood tests. It be applied to differential signal analysis of -other types of genomic data that produce counts, including ChIP-seq, SAGE and -CAGE.") - (license license:gpl2+))) - (define-public r-variantannotation (package (name "r-variantannotation") -- cgit v1.2.3 From bf612ead766ee5afcdccd7c8ab003b791ecea9df Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 14:01:58 +0100 Subject: gnu: r-variantannotation: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-variantannotation): Move from here... * gnu/packages/bioconductor.scm (r-variantannotation): ...to here. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 -------------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fb0127b7ca..c4df090a05 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2051,6 +2051,44 @@ experimental designs is facilitated by a consistently implemented sample annotation infrastructure.") (license license:artistic2.0))) +(define-public r-variantannotation + (package + (name "r-variantannotation") + (version "1.36.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "VariantAnnotation" version)) + (sha256 + (base32 + "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) + (properties + `((upstream-name . "VariantAnnotation"))) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-bsgenome" ,r-bsgenome) + ("r-dbi" ,r-dbi) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicfeatures" ,r-genomicfeatures) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-matrixgenerics" ,r-matrixgenerics) + ("r-summarizedexperiment" ,r-summarizedexperiment) + ("r-rhtslib" ,r-rhtslib) + ("r-rsamtools" ,r-rsamtools) + ("r-rtracklayer" ,r-rtracklayer) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector) + ("r-zlibbioc" ,r-zlibbioc))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/VariantAnnotation") + (synopsis "Package for annotation of genetic variants") + (description "This R package can annotate variants, compute amino acid +coding changes and predict coding outcomes.") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dc0d7a2906..78df3091fe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-variantannotation - (package - (name "r-variantannotation") - (version "1.36.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "VariantAnnotation" version)) - (sha256 - (base32 - "1sl0l6v05lfglj281nszma0h5k234md7rn2pdah8vs2d4iq3kimw")))) - (properties - `((upstream-name . "VariantAnnotation"))) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-biostrings" ,r-biostrings) - ("r-bsgenome" ,r-bsgenome) - ("r-dbi" ,r-dbi) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicfeatures" ,r-genomicfeatures) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-matrixgenerics" ,r-matrixgenerics) - ("r-summarizedexperiment" ,r-summarizedexperiment) - ("r-rhtslib" ,r-rhtslib) - ("r-rsamtools" ,r-rsamtools) - ("r-rtracklayer" ,r-rtracklayer) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector) - ("r-zlibbioc" ,r-zlibbioc))) - (build-system r-build-system) - (home-page "https://bioconductor.org/packages/VariantAnnotation") - (synopsis "Package for annotation of genetic variants") - (description "This R package can annotate variants, compute amino acid -coding changes and predict coding outcomes.") - (license license:artistic2.0))) - (define-public r-limma (package (name "r-limma") -- cgit v1.2.3 From f10f2745eb1ec38eae5c41323f31980d2dd1f38c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 15 Mar 2021 15:02:40 +0100 Subject: gnu: r-delayedarray: Update to 0.16.2. * gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 78df3091fe..996a3614e7 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7966,13 +7966,13 @@ tab-delimited (tabix) files.") (define-public r-delayedarray (package (name "r-delayedarray") - (version "0.16.1") + (version "0.16.2") (source (origin (method url-fetch) (uri (bioconductor-uri "DelayedArray" version)) (sha256 (base32 - "1d75zrhha1v7dhbvjp6a4iap441l5k268w0jjxklpqywbqns7l3d")))) + "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) (properties `((upstream-name . "DelayedArray"))) (build-system r-build-system) -- cgit v1.2.3 From 14204d696c6fc0e49be93981328bc5148907aee7 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 15 Mar 2021 15:02:43 +0100 Subject: gnu: r-genomicfeatures: Update to 1.42.2. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.42.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 996a3614e7..d9afe2c56f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8114,13 +8114,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.42.1") + (version "1.42.2") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "17dyd9hcw6pw16y353dh55wfhxmkxka99lbsxsp9xyrhffwrxi0s")))) + "17ns5hvx5q8mrmkgb6linspwml62mi34i6al5bxlib5xi9d9f04s")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From 821e6439212f8e94580674eaaff2ce6752cd3b18 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:08:55 +0100 Subject: gnu: r-limma: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-limma): Move from here... * gnu/packages/bioconductor.scm (r-limma): ...to here. --- gnu/packages/bioconductor.scm | 19 +++++++++++++++++++ gnu/packages/bioinformatics.scm | 19 ------------------- 2 files changed, 19 insertions(+), 19 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d611f3a491..379b6c30c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1850,6 +1850,25 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-limma + (package + (name "r-limma") + (version "3.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "limma" version)) + (sha256 + (base32 + "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) + (build-system r-build-system) + (home-page "http://bioinf.wehi.edu.au/limma") + (synopsis "Package for linear models for microarray and RNA-seq data") + (description "This package can be used for the analysis of gene expression +studies, especially the use of linear models for analysing designed experiments +and the assessment of differential expression. The analysis methods apply to +different technologies, including microarrays, RNA-seq, and quantitative PCR.") + (license license:gpl2+))) + (define-public r-rbgl (package (name "r-rbgl") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d9afe2c56f..9774b442a3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,25 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-limma - (package - (name "r-limma") - (version "3.46.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "limma" version)) - (sha256 - (base32 - "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) - (build-system r-build-system) - (home-page "http://bioinf.wehi.edu.au/limma") - (synopsis "Package for linear models for microarray and RNA-seq data") - (description "This package can be used for the analysis of gene expression -studies, especially the use of linear models for analysing designed experiments -and the assessment of differential expression. The analysis methods apply to -different technologies, including microarrays, RNA-seq, and quantitative PCR.") - (license license:gpl2+))) - (define-public r-xvector (package (name "r-xvector") -- cgit v1.2.3 From e56b3db82ea81e88632a15994a5792849ecb0c5c Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:08:56 +0100 Subject: gnu: r-xvector: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-xvector): Move from here... * gnu/packages/bioconductor.scm (r-xvector): ...to here. --- gnu/packages/bioconductor.scm | 36 ++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 36 ------------------------------------ 2 files changed, 36 insertions(+), 36 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 379b6c30c0..fdb2f7c7ac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2108,6 +2108,42 @@ annotation infrastructure.") coding changes and predict coding outcomes.") (license license:artistic2.0))) +(define-public r-xvector + (package + (name "r-xvector") + (version "0.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "XVector" version)) + (sha256 + (base32 + "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) + (properties + `((upstream-name . "XVector"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/XVector") + (synopsis "Representation and manpulation of external sequences") + (description + "This package provides memory efficient S4 classes for storing sequences +\"externally\" (behind an R external pointer, or on disk).") + (license license:artistic2.0))) + (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9774b442a3..65db983461 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,42 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-xvector - (package - (name "r-xvector") - (version "0.30.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "XVector" version)) - (sha256 - (base32 - "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) - (properties - `((upstream-name . "XVector"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/XVector") - (synopsis "Representation and manpulation of external sequences") - (description - "This package provides memory efficient S4 classes for storing sequences -\"externally\" (behind an R external pointer, or on disk).") - (license license:artistic2.0))) - (define-public r-genomicranges (package (name "r-genomicranges") -- cgit v1.2.3 From f3f09b99cd32f46c47db30f0afb632614c43172d Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:08:57 +0100 Subject: gnu: r-genomicranges: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-genomicranges): Move from here... * gnu/packages/bioconductor.scm (r-genomicranges): ...to here. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 31 ------------------------------- 2 files changed, 31 insertions(+), 31 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fdb2f7c7ac..ec273cae70 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1770,6 +1770,37 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) +(define-public r-genomicranges + (package + (name "r-genomicranges") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicRanges" version)) + (sha256 + (base32 + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + (properties + `((upstream-name . "GenomicRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicRanges") + (synopsis "Representation and manipulation of genomic intervals") + (description + "This package provides tools to efficiently represent and manipulate +genomic annotations and alignments is playing a central role when it comes to +analyzing high-throughput sequencing data (a.k.a. NGS data). The +GenomicRanges package defines general purpose containers for storing and +manipulating genomic intervals and variables defined along a genome.") + (license license:artistic2.0))) + (define-public r-gostats (package (name "r-gostats") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65db983461..4889c148e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,37 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-genomicranges - (package - (name "r-genomicranges") - (version "1.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicRanges" version)) - (sha256 - (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) - (properties - `((upstream-name . "GenomicRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicRanges") - (synopsis "Representation and manipulation of genomic intervals") - (description - "This package provides tools to efficiently represent and manipulate -genomic annotations and alignments is playing a central role when it comes to -analyzing high-throughput sequencing data (a.k.a. NGS data). The -GenomicRanges package defines general purpose containers for storing and -manipulating genomic intervals and variables defined along a genome.") - (license license:artistic2.0))) - (define-public r-biobase (package (name "r-biobase") -- cgit v1.2.3 From 457de7f401300085066a0426068fe75f8df85943 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:08:58 +0100 Subject: gnu: r-biobase: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biobase): Move from here... * gnu/packages/bioconductor.scm (r-biobase): ...to here. --- gnu/packages/bioconductor.scm | 22 ++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 22 ---------------------- 2 files changed, 22 insertions(+), 22 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index ec273cae70..b7308848c0 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1570,6 +1570,28 @@ microarrays.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) +(define-public r-biobase + (package + (name "r-biobase") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biobase" version)) + (sha256 + (base32 + "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) + (properties + `((upstream-name . "Biobase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/Biobase") + (synopsis "Base functions for Bioconductor") + (description + "This package provides functions that are needed by many other packages +on Bioconductor or which replace R functions.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4889c148e4..b73862ff86 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,28 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biobase - (package - (name "r-biobase") - (version "2.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biobase" version)) - (sha256 - (base32 - "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) - (properties - `((upstream-name . "Biobase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/Biobase") - (synopsis "Base functions for Bioconductor") - (description - "This package provides functions that are needed by many other packages -on Bioconductor or which replace R functions.") - (license license:artistic2.0))) - (define-public r-annotationdbi (package (name "r-annotationdbi") -- cgit v1.2.3 From 16c7e79ebbe911a1e8cb7ad8d9cb1c5d8ede34c7 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:08:59 +0100 Subject: gnu: r-annotationdbi: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-annotationdbi): Move from here... * gnu/packages/bioconductor.scm (r-annotationdbi): ...to here. --- gnu/packages/bioconductor.scm | 29 +++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 29 ----------------------------- 2 files changed, 29 insertions(+), 29 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b7308848c0..2ae212dfac 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1538,6 +1538,35 @@ structure.") microarrays.") (license license:artistic2.0))) +(define-public r-annotationdbi + (package + (name "r-annotationdbi") + (version "1.52.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationDbi" version)) + (sha256 + (base32 + "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) + (properties + `((upstream-name . "AnnotationDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationDbi") + (synopsis "Annotation database interface") + (description + "This package provides user interface and database connection code for +annotation data packages using SQLite data storage.") + (license license:artistic2.0))) + (define-public r-annotationforge (package (name "r-annotationforge") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b73862ff86..a45196bc5b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,35 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-annotationdbi - (package - (name "r-annotationdbi") - (version "1.52.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationDbi" version)) - (sha256 - (base32 - "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) - (properties - `((upstream-name . "AnnotationDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationDbi") - (synopsis "Annotation database interface") - (description - "This package provides user interface and database connection code for -annotation data packages using SQLite data storage.") - (license license:artistic2.0))) - (define-public r-biomart (package (name "r-biomart") -- cgit v1.2.3 From c11b541fba8131e701b55c5c7ef1a412bb4d1fc8 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:09:00 +0100 Subject: gnu: r-biomart: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biomart): Move from here... * gnu/packages/bioconductor.scm (r-biomart): ...to here. --- gnu/packages/bioconductor.scm | 38 ++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 38 -------------------------------------- 2 files changed, 38 insertions(+), 38 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2ae212dfac..897e85dfe3 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1621,6 +1621,44 @@ databases. Packages produced are intended to be used with AnnotationDbi.") on Bioconductor or which replace R functions.") (license license:artistic2.0))) +(define-public r-biomart + (package + (name "r-biomart") + (version "2.46.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biomaRt" version)) + (sha256 + (base32 + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + (properties + `((upstream-name . "biomaRt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) + ("r-progress" ,r-progress) + ("r-rappdirs" ,r-rappdirs) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biomaRt") + (synopsis "Interface to BioMart databases") + (description + "biomaRt provides an interface to a growing collection of databases +implementing the @url{BioMart software suite, http://www.biomart.org}. The +package enables retrieval of large amounts of data in a uniform way without +the need to know the underlying database schemas or write complex SQL queries. +Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, +Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt +users direct access to a diverse set of data and enable a wide range of +powerful online queries from gene annotation to database mining.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a45196bc5b..289a96f572 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,44 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biomart - (package - (name "r-biomart") - (version "2.46.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biomaRt" version)) - (sha256 - (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) - (properties - `((upstream-name . "biomaRt"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/biomaRt") - (synopsis "Interface to BioMart databases") - (description - "biomaRt provides an interface to a growing collection of databases -implementing the @url{BioMart software suite, http://www.biomart.org}. The -package enables retrieval of large amounts of data in a uniform way without -the need to know the underlying database schemas or write complex SQL queries. -Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, -Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt -users direct access to a diverse set of data and enable a wide range of -powerful online queries from gene annotation to database mining.") - (license license:artistic2.0))) - (define-public r-biocparallel (package (name "r-biocparallel") -- cgit v1.2.3 From eab9807fb38b70e203ac965f2705c76adaedcc07 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:09:01 +0100 Subject: gnu: r-biocparallel: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biocparallel): Move from here... * gnu/packages/bioconductor.scm (r-biocparallel): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 897e85dfe3..6482d8e4c1 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1659,6 +1659,33 @@ users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.") (license license:artistic2.0))) +(define-public r-biocparallel + (package + (name "r-biocparallel") + (version "1.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocParallel" version)) + (sha256 + (base32 + "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) + (properties + `((upstream-name . "BiocParallel"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-logger" ,r-futile-logger) + ("r-snow" ,r-snow) + ("r-bh" ,r-bh))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocParallel") + (synopsis "Bioconductor facilities for parallel evaluation") + (description + "This package provides modified versions and novel implementation of +functions for parallel evaluation, tailored to use with Bioconductor +objects.") + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 289a96f572..af3fa36b19 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,33 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biocparallel - (package - (name "r-biocparallel") - (version "1.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocParallel" version)) - (sha256 - (base32 - "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) - (properties - `((upstream-name . "BiocParallel"))) - (build-system r-build-system) - (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocParallel") - (synopsis "Bioconductor facilities for parallel evaluation") - (description - "This package provides modified versions and novel implementation of -functions for parallel evaluation, tailored to use with Bioconductor -objects.") - (license (list license:gpl2+ license:gpl3+)))) - (define-public r-biostrings (package (name "r-biostrings") -- cgit v1.2.3 From b1a19ab6e28277f0f9c72961be3cf709bd14e6e2 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:09:02 +0100 Subject: gnu: r-biostrings: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-biostrings): Move from here... * gnu/packages/bioconductor.scm (r-biostrings): ...to here. --- gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 27 --------------------------- 2 files changed, 27 insertions(+), 27 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6482d8e4c1..2b7d65023d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1686,6 +1686,33 @@ functions for parallel evaluation, tailored to use with Bioconductor objects.") (license (list license:gpl2+ license:gpl3+)))) +(define-public r-biostrings + (package + (name "r-biostrings") + (version "2.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biostrings" version)) + (sha256 + (base32 + "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) + (properties + `((upstream-name . "Biostrings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-crayon" ,r-crayon) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/Biostrings") + (synopsis "String objects and algorithms for biological sequences") + (description + "This package provides memory efficient string containers, string +matching algorithms, and other utilities, for fast manipulation of large +biological sequences or sets of sequences.") + (license license:artistic2.0))) + (define-public r-category (package (name "r-category") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index af3fa36b19..415210085e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,33 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-biostrings - (package - (name "r-biostrings") - (version "2.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biostrings" version)) - (sha256 - (base32 - "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) - (properties - `((upstream-name . "Biostrings"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/Biostrings") - (synopsis "String objects and algorithms for biological sequences") - (description - "This package provides memory efficient string containers, string -matching algorithms, and other utilities, for fast manipulation of large -biological sequences or sets of sequences.") - (license license:artistic2.0))) - (define-public r-rsamtools (package (name "r-rsamtools") -- cgit v1.2.3 From adf45daae93219a31dbabd8dd80a806cc747aa81 Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:09:03 +0100 Subject: gnu: r-rsamtools: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-rsamtools): Move from here... * gnu/packages/bioconductor.scm (r-rsamtools): ...to here. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 43 ----------------------------------------- 2 files changed, 43 insertions(+), 43 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2b7d65023d..c659bdd09e 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -2147,6 +2147,49 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + (properties + `((upstream-name . "Rsamtools"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the @code{samtools}, +@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence +Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed +tab-delimited (tabix) files.") + (license license:expat))) + (define-public r-shortread (package (name "r-shortread") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 415210085e..05805d1a8b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,49 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-rsamtools - (package - (name "r-rsamtools") - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Rsamtools" version)) - (sha256 - (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) - (properties - `((upstream-name . "Rsamtools"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") - (synopsis "Interface to samtools, bcftools, and tabix") - (description - "This package provides an interface to the @code{samtools}, -@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence -Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed -tab-delimited (tabix) files.") - (license license:expat))) - (define-public r-delayedarray (package (name "r-delayedarray") -- cgit v1.2.3 From d99a18252c31fb2c19e3e7ae65bb36e85c3aa1af Mon Sep 17 00:00:00 2001 From: zimoun Date: Mon, 15 Mar 2021 19:09:04 +0100 Subject: gnu: r-delayedarray: Move to (gnu packages bioconductor). * gnu/packages/bioinformatics.scm (r-delayedarray): Move from here... * gnu/packages/bioconductor.scm (r-delayedarray): ...to here. --- gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++ gnu/packages/bioinformatics.scm | 33 --------------------------------- 2 files changed, 33 insertions(+), 33 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c659bdd09e..9212165706 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1212,6 +1212,39 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) +(define-public r-delayedarray + (package + (name "r-delayedarray") + (version "0.16.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedArray" version)) + (sha256 + (base32 + "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) + (properties + `((upstream-name . "DelayedArray"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DelayedArray") + (synopsis "Delayed operations on array-like objects") + (description + "Wrapping an array-like object (typically an on-disk object) in a +@code{DelayedArray} object allows one to perform common array operations on it +without loading the object in memory. In order to reduce memory usage and +optimize performance, operations on the object are either delayed or executed +using a block processing mechanism. Note that this also works on in-memory +array-like objects like @code{DataFrame} objects (typically with Rle columns), +@code{Matrix} objects, and ordinary arrays and data frames.") + (license license:artistic2.0))) + (define-public r-bluster (package (name "r-bluster") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 05805d1a8b..bc342b5de8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,39 +7691,6 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) -(define-public r-delayedarray - (package - (name "r-delayedarray") - (version "0.16.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "DelayedArray" version)) - (sha256 - (base32 - "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) - (properties - `((upstream-name . "DelayedArray"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DelayedArray") - (synopsis "Delayed operations on array-like objects") - (description - "Wrapping an array-like object (typically an on-disk object) in a -@code{DelayedArray} object allows one to perform common array operations on it -without loading the object in memory. In order to reduce memory usage and -optimize performance, operations on the object are either delayed or executed -using a block processing mechanism. Note that this also works on in-memory -array-like objects like @code{DataFrame} objects (typically with Rle columns), -@code{Matrix} objects, and ordinary arrays and data frames.") - (license license:artistic2.0))) - (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") -- cgit v1.2.3 From 8ec0ca8faff62f19426f22aeb1bd59a8950ca05a Mon Sep 17 00:00:00 2001 From: Leo Famulari Date: Mon, 15 Mar 2021 19:48:52 -0400 Subject: Revert some commits that caused `guix pull` to fail. This reverts commits 821e6439212f8e94580674eaaff2ce6752cd3b18 through 8f9fd9b70c7bf166d96a4b1dc8b427f8cdf040b5. Specifically, these commits caused the build failure of guix-package-cache.drv like this: ------ (repl-version 0 1 1) Generating package cache for '/gnu/store/vyz7q26kxxd4z70m24rkkqqhaizdla7g-profile'... (exception unbound-variable (value #f) (value "Unbound variable: ~S") (value (r-biobase)) (value #f)) --- gnu/packages/bioconductor.scm | 333 ---------------------------------------- gnu/packages/bioinformatics.scm | 305 ++++++++++++++++++++++++++++++++++++ 2 files changed, 305 insertions(+), 333 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 166d30be0f..d611f3a491 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1212,39 +1212,6 @@ data. In addition, provides numerous plotting functions for commonly used visualizations.") (license license:artistic2.0))) -(define-public r-delayedarray - (package - (name "r-delayedarray") - (version "0.16.2") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "DelayedArray" version)) - (sha256 - (base32 - "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) - (properties - `((upstream-name . "DelayedArray"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-s4vectors" ,r-s4vectors) - ("r-iranges" ,r-iranges) - ("r-matrix" ,r-matrix) - ("r-matrixgenerics" ,r-matrixgenerics))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/DelayedArray") - (synopsis "Delayed operations on array-like objects") - (description - "Wrapping an array-like object (typically an on-disk object) in a -@code{DelayedArray} object allows one to perform common array operations on it -without loading the object in memory. In order to reduce memory usage and -optimize performance, operations on the object are either delayed or executed -using a block processing mechanism. Note that this also works on in-memory -array-like objects like @code{DataFrame} objects (typically with Rle columns), -@code{Matrix} objects, and ordinary arrays and data frames.") - (license license:artistic2.0))) - (define-public r-bluster (package (name "r-bluster") @@ -1571,35 +1538,6 @@ structure.") microarrays.") (license license:artistic2.0))) -(define-public r-annotationdbi - (package - (name "r-annotationdbi") - (version "1.52.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "AnnotationDbi" version)) - (sha256 - (base32 - "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) - (properties - `((upstream-name . "AnnotationDbi"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biobase" ,r-biobase) - ("r-biocgenerics" ,r-biocgenerics) - ("r-dbi" ,r-dbi) - ("r-iranges" ,r-iranges) - ("r-rsqlite" ,r-rsqlite) - ("r-s4vectors" ,r-s4vectors))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/AnnotationDbi") - (synopsis "Annotation database interface") - (description - "This package provides user interface and database connection code for -annotation data packages using SQLite data storage.") - (license license:artistic2.0))) - (define-public r-annotationforge (package (name "r-annotationforge") @@ -1632,148 +1570,6 @@ annotation data packages using SQLite data storage.") databases. Packages produced are intended to be used with AnnotationDbi.") (license license:artistic2.0))) -(define-public r-biobase - (package - (name "r-biobase") - (version "2.50.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biobase" version)) - (sha256 - (base32 - "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) - (properties - `((upstream-name . "Biobase"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics))) - (home-page "https://bioconductor.org/packages/Biobase") - (synopsis "Base functions for Bioconductor") - (description - "This package provides functions that are needed by many other packages -on Bioconductor or which replace R functions.") - (license license:artistic2.0))) - -(define-public r-biomart - (package - (name "r-biomart") - (version "2.46.3") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "biomaRt" version)) - (sha256 - (base32 - "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) - (properties - `((upstream-name . "biomaRt"))) - (build-system r-build-system) - (propagated-inputs - `(("r-annotationdbi" ,r-annotationdbi) - ("r-biocfilecache" ,r-biocfilecache) - ("r-httr" ,r-httr) - ("r-openssl" ,r-openssl) - ("r-progress" ,r-progress) - ("r-rappdirs" ,r-rappdirs) - ("r-stringr" ,r-stringr) - ("r-xml" ,r-xml) - ("r-xml2" ,r-xml2))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/biomaRt") - (synopsis "Interface to BioMart databases") - (description - "biomaRt provides an interface to a growing collection of databases -implementing the @url{BioMart software suite, http://www.biomart.org}. The -package enables retrieval of large amounts of data in a uniform way without -the need to know the underlying database schemas or write complex SQL queries. -Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, -Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt -users direct access to a diverse set of data and enable a wide range of -powerful online queries from gene annotation to database mining.") - (license license:artistic2.0))) - -(define-public r-biocparallel - (package - (name "r-biocparallel") - (version "1.24.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "BiocParallel" version)) - (sha256 - (base32 - "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) - (properties - `((upstream-name . "BiocParallel"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'make-reproducible - (lambda _ - ;; Remove generated documentation. - (for-each delete-file - '("inst/doc/BiocParallel_BatchtoolsParam.pdf" - "inst/doc/Introduction_To_BiocParallel.pdf" - "inst/doc/Errors_Logs_And_Debugging.pdf" - "inst/doc/BiocParallel_BatchtoolsParam.R" - "inst/doc/Introduction_To_BiocParallel.R" - "inst/doc/Errors_Logs_And_Debugging.R")) - - ;; Remove time-dependent macro - (substitute* '("inst/doc/BiocParallel_BatchtoolsParam.Rnw" - "inst/doc/Introduction_To_BiocParallel.Rnw" - "inst/doc/Errors_Logs_And_Debugging.Rnw" - "vignettes/BiocParallel_BatchtoolsParam.Rnw" - "vignettes/Introduction_To_BiocParallel.Rnw" - "vignettes/Errors_Logs_And_Debugging.Rnw") - (("\\today") "later")) - - ;; Initialize the random number generator seed when building. - (substitute* "R/internal_rng_stream.R" - (("\"L'Ecuyer-CMRG\"\\)" m) - (string-append - m "; if (!is.na(Sys.getenv(\"SOURCE_DATE_EPOCH\"))) {set.seed(100)}\n")))))))) - (propagated-inputs - `(("r-futile-logger" ,r-futile-logger) - ("r-snow" ,r-snow) - ("r-bh" ,r-bh))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/BiocParallel") - (synopsis "Bioconductor facilities for parallel evaluation") - (description - "This package provides modified versions and novel implementation of -functions for parallel evaluation, tailored to use with Bioconductor -objects.") - (license (list license:gpl2+ license:gpl3+)))) - -(define-public r-biostrings - (package - (name "r-biostrings") - (version "2.58.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Biostrings" version)) - (sha256 - (base32 - "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) - (properties - `((upstream-name . "Biostrings"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-crayon" ,r-crayon) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/Biostrings") - (synopsis "String objects and algorithms for biological sequences") - (description - "This package provides memory efficient string containers, string -matching algorithms, and other utilities, for fast manipulation of large -biological sequences or sets of sequences.") - (license license:artistic2.0))) - (define-public r-category (package (name "r-category") @@ -1974,37 +1770,6 @@ translation between different chromosome sequence naming conventions (e.g., names in their natural, rather than lexicographic, order.") (license license:artistic2.0))) -(define-public r-genomicranges - (package - (name "r-genomicranges") - (version "1.42.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "GenomicRanges" version)) - (sha256 - (base32 - "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) - (properties - `((upstream-name . "GenomicRanges"))) - (build-system r-build-system) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (native-inputs - `(("r-knitr" ,r-knitr))) - (home-page "https://bioconductor.org/packages/GenomicRanges") - (synopsis "Representation and manipulation of genomic intervals") - (description - "This package provides tools to efficiently represent and manipulate -genomic annotations and alignments is playing a central role when it comes to -analyzing high-throughput sequencing data (a.k.a. NGS data). The -GenomicRanges package defines general purpose containers for storing and -manipulating genomic intervals and variables defined along a genome.") - (license license:artistic2.0))) - (define-public r-gostats (package (name "r-gostats") @@ -2085,25 +1850,6 @@ Enrichment Analysis} (GSEA).") the Human Protein Atlas project.") (license license:artistic2.0))) -(define-public r-limma - (package - (name "r-limma") - (version "3.46.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "limma" version)) - (sha256 - (base32 - "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) - (build-system r-build-system) - (home-page "http://bioinf.wehi.edu.au/limma") - (synopsis "Package for linear models for microarray and RNA-seq data") - (description "This package can be used for the analysis of gene expression -studies, especially the use of linear models for analysing designed experiments -and the assessment of differential expression. The analysis methods apply to -different technologies, including microarrays, RNA-seq, and quantitative PCR.") - (license license:gpl2+))) - (define-public r-rbgl (package (name "r-rbgl") @@ -2208,49 +1954,6 @@ reports together for a particular project that can be viewed in a web browser.") (license license:artistic2.0))) -(define-public r-rsamtools - (package - (name "r-rsamtools") - (version "2.6.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "Rsamtools" version)) - (sha256 - (base32 - "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) - (properties - `((upstream-name . "Rsamtools"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-biocparallel" ,r-biocparallel) - ("r-biostrings" ,r-biostrings) - ("r-bitops" ,r-bitops) - ("r-genomeinfodb" ,r-genomeinfodb) - ("r-genomicranges" ,r-genomicranges) - ("r-iranges" ,r-iranges) - ("r-rhtslib" ,r-rhtslib) - ("r-s4vectors" ,r-s4vectors) - ("r-xvector" ,r-xvector))) - (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") - (synopsis "Interface to samtools, bcftools, and tabix") - (description - "This package provides an interface to the @code{samtools}, -@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence -Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed -tab-delimited (tabix) files.") - (license license:expat))) - (define-public r-shortread (package (name "r-shortread") @@ -2386,42 +2089,6 @@ annotation infrastructure.") coding changes and predict coding outcomes.") (license license:artistic2.0))) -(define-public r-xvector - (package - (name "r-xvector") - (version "0.30.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "XVector" version)) - (sha256 - (base32 - "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) - (properties - `((upstream-name . "XVector"))) - (build-system r-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'use-system-zlib - (lambda _ - (substitute* "DESCRIPTION" - (("zlibbioc, ") "")) - (substitute* "NAMESPACE" - (("import\\(zlibbioc\\)") "")) - #t))))) - (inputs - `(("zlib" ,zlib))) - (propagated-inputs - `(("r-biocgenerics" ,r-biocgenerics) - ("r-iranges" ,r-iranges) - ("r-s4vectors" ,r-s4vectors))) - (home-page "https://bioconductor.org/packages/XVector") - (synopsis "Representation and manpulation of external sequences") - (description - "This package provides memory efficient S4 classes for storing sequences -\"externally\" (behind an R external pointer, or on disk).") - (license license:artistic2.0))) - (define-public r-geneplotter (package (name "r-geneplotter") diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bc342b5de8..d9afe2c56f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,6 +7691,311 @@ including VCF header and contents in RDF and JSON.") (home-page "https://github.com/vcflib/bio-vcf") (license license:expat))) +(define-public r-limma + (package + (name "r-limma") + (version "3.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "limma" version)) + (sha256 + (base32 + "1xxv493q1kip9bjfv7v7k5dnq7hz7gvl80i983v4mvwavhgnbxfz")))) + (build-system r-build-system) + (home-page "http://bioinf.wehi.edu.au/limma") + (synopsis "Package for linear models for microarray and RNA-seq data") + (description "This package can be used for the analysis of gene expression +studies, especially the use of linear models for analysing designed experiments +and the assessment of differential expression. The analysis methods apply to +different technologies, including microarrays, RNA-seq, and quantitative PCR.") + (license license:gpl2+))) + +(define-public r-xvector + (package + (name "r-xvector") + (version "0.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "XVector" version)) + (sha256 + (base32 + "1pqljikg4f6jb7wgm5537zwgq5b013nyz1agjrwfq2cljb0ym6lq")))) + (properties + `((upstream-name . "XVector"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (inputs + `(("zlib" ,zlib))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors))) + (home-page "https://bioconductor.org/packages/XVector") + (synopsis "Representation and manpulation of external sequences") + (description + "This package provides memory efficient S4 classes for storing sequences +\"externally\" (behind an R external pointer, or on disk).") + (license license:artistic2.0))) + +(define-public r-genomicranges + (package + (name "r-genomicranges") + (version "1.42.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicRanges" version)) + (sha256 + (base32 + "0j4py5g6pdj35xhlaqhxxhg55j9l4mcdk3yck4dgyavv5f2dh24i")))) + (properties + `((upstream-name . "GenomicRanges"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/GenomicRanges") + (synopsis "Representation and manipulation of genomic intervals") + (description + "This package provides tools to efficiently represent and manipulate +genomic annotations and alignments is playing a central role when it comes to +analyzing high-throughput sequencing data (a.k.a. NGS data). The +GenomicRanges package defines general purpose containers for storing and +manipulating genomic intervals and variables defined along a genome.") + (license license:artistic2.0))) + +(define-public r-biobase + (package + (name "r-biobase") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biobase" version)) + (sha256 + (base32 + "11kgc4flywlm3i18603558l8ksv91c24vkc5fnnbcd375i2dhhd4")))) + (properties + `((upstream-name . "Biobase"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics))) + (home-page "https://bioconductor.org/packages/Biobase") + (synopsis "Base functions for Bioconductor") + (description + "This package provides functions that are needed by many other packages +on Bioconductor or which replace R functions.") + (license license:artistic2.0))) + +(define-public r-annotationdbi + (package + (name "r-annotationdbi") + (version "1.52.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnnotationDbi" version)) + (sha256 + (base32 + "0zqxgh3nx6y8ry12s2vss2f4axz5vpqxha1y4ifhhcx4zhpzsglr")))) + (properties + `((upstream-name . "AnnotationDbi"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-dbi" ,r-dbi) + ("r-iranges" ,r-iranges) + ("r-rsqlite" ,r-rsqlite) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/AnnotationDbi") + (synopsis "Annotation database interface") + (description + "This package provides user interface and database connection code for +annotation data packages using SQLite data storage.") + (license license:artistic2.0))) + +(define-public r-biomart + (package + (name "r-biomart") + (version "2.46.3") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "biomaRt" version)) + (sha256 + (base32 + "0gwmd0ykpv0gyh34c56g5m12lil20fvig49f3ih1jxrxf3q4wmq7")))) + (properties + `((upstream-name . "biomaRt"))) + (build-system r-build-system) + (propagated-inputs + `(("r-annotationdbi" ,r-annotationdbi) + ("r-biocfilecache" ,r-biocfilecache) + ("r-httr" ,r-httr) + ("r-openssl" ,r-openssl) + ("r-progress" ,r-progress) + ("r-rappdirs" ,r-rappdirs) + ("r-stringr" ,r-stringr) + ("r-xml" ,r-xml) + ("r-xml2" ,r-xml2))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/biomaRt") + (synopsis "Interface to BioMart databases") + (description + "biomaRt provides an interface to a growing collection of databases +implementing the @url{BioMart software suite, http://www.biomart.org}. The +package enables retrieval of large amounts of data in a uniform way without +the need to know the underlying database schemas or write complex SQL queries. +Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, +Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt +users direct access to a diverse set of data and enable a wide range of +powerful online queries from gene annotation to database mining.") + (license license:artistic2.0))) + +(define-public r-biocparallel + (package + (name "r-biocparallel") + (version "1.24.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BiocParallel" version)) + (sha256 + (base32 + "1iryicvmcagcrj29kp49mqhiq2kn72j4idj380hi9illmdrg9ism")))) + (properties + `((upstream-name . "BiocParallel"))) + (build-system r-build-system) + (propagated-inputs + `(("r-futile-logger" ,r-futile-logger) + ("r-snow" ,r-snow) + ("r-bh" ,r-bh))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/BiocParallel") + (synopsis "Bioconductor facilities for parallel evaluation") + (description + "This package provides modified versions and novel implementation of +functions for parallel evaluation, tailored to use with Bioconductor +objects.") + (license (list license:gpl2+ license:gpl3+)))) + +(define-public r-biostrings + (package + (name "r-biostrings") + (version "2.58.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Biostrings" version)) + (sha256 + (base32 + "1rbqhs73mhfr1gi0rx28jiyan7i3hb45ai3jpl1656fnrhgjfxq5")))) + (properties + `((upstream-name . "Biostrings"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-crayon" ,r-crayon) + ("r-iranges" ,r-iranges) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/Biostrings") + (synopsis "String objects and algorithms for biological sequences") + (description + "This package provides memory efficient string containers, string +matching algorithms, and other utilities, for fast manipulation of large +biological sequences or sets of sequences.") + (license license:artistic2.0))) + +(define-public r-rsamtools + (package + (name "r-rsamtools") + (version "2.6.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Rsamtools" version)) + (sha256 + (base32 + "040pggkwglc6wy90qnc7xcdnaj0v3iqlykvvsl74241409qly554")))) + (properties + `((upstream-name . "Rsamtools"))) + (build-system r-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'use-system-zlib + (lambda _ + (substitute* "DESCRIPTION" + (("zlibbioc, ") "")) + (substitute* "NAMESPACE" + (("import\\(zlibbioc\\)") "")) + #t))))) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-biocparallel" ,r-biocparallel) + ("r-biostrings" ,r-biostrings) + ("r-bitops" ,r-bitops) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-iranges" ,r-iranges) + ("r-rhtslib" ,r-rhtslib) + ("r-s4vectors" ,r-s4vectors) + ("r-xvector" ,r-xvector))) + (home-page "https://bioconductor.org/packages/release/bioc/html/Rsamtools.html") + (synopsis "Interface to samtools, bcftools, and tabix") + (description + "This package provides an interface to the @code{samtools}, +@code{bcftools}, and @code{tabix} utilities for manipulating SAM (Sequence +Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed +tab-delimited (tabix) files.") + (license license:expat))) + +(define-public r-delayedarray + (package + (name "r-delayedarray") + (version "0.16.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DelayedArray" version)) + (sha256 + (base32 + "09lpj951v1afxkrnjvnhzp4qgklq23ykdwlny7k1lyfcdy9q6wm0")))) + (properties + `((upstream-name . "DelayedArray"))) + (build-system r-build-system) + (propagated-inputs + `(("r-biocgenerics" ,r-biocgenerics) + ("r-s4vectors" ,r-s4vectors) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-matrixgenerics" ,r-matrixgenerics))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/DelayedArray") + (synopsis "Delayed operations on array-like objects") + (description + "Wrapping an array-like object (typically an on-disk object) in a +@code{DelayedArray} object allows one to perform common array operations on it +without loading the object in memory. In order to reduce memory usage and +optimize performance, operations on the object are either delayed or executed +using a block processing mechanism. Note that this also works on in-memory +array-like objects like @code{DataFrame} objects (typically with Rle columns), +@code{Matrix} objects, and ordinary arrays and data frames.") + (license license:artistic2.0))) + (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") -- cgit v1.2.3 From fcf8c6c5652cac87647d87e87dede3a7b154716b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 16 Mar 2021 11:03:58 +0100 Subject: gnu: hisat2: Update to 2.2.1. * gnu/packages/bioinformatics.scm (hisat2): Update to 2.2.1. [source]: Fetch from git repository on Github. [arguments]: Add phase to build manual; remove trailing #t from other phases. [native-inputs]: Remove unzip. [home-page]: Update. [inputs]: Add python-wrapper. --- gnu/packages/bioinformatics.scm | 29 +++++++++++++++++------------ 1 file changed, 17 insertions(+), 12 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d9afe2c56f..90e81354a5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3819,15 +3819,17 @@ particular, reads spanning multiple exons.") (define-public hisat2 (package (name "hisat2") - (version "2.0.5") + (version "2.2.1") (source (origin - (method url-fetch) - (uri (string-append "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2" - "/downloads/hisat2-" version "-source.zip")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/DaehwanKimLab/hisat2/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "0lywnr8kijwsc2aw10dwxic0n0yvip6fl3rjlvc8zzwahamy4x7g")))) + "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -3840,9 +3842,12 @@ particular, reads spanning multiple exons.") (add-after 'unpack 'make-deterministic (lambda _ (substitute* "Makefile" - (("`date`") "0")) - #t)) + (("`date`") "0")))) (delete 'configure) + (add-before 'build 'build-manual + (lambda _ + (mkdir-p "doc") + (invoke "make" "doc"))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) @@ -3853,13 +3858,13 @@ particular, reads spanning multiple exons.") (find-files "." "hisat2(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")) (mkdir-p doc) - (install-file "doc/manual.inc.html" doc)) - #t))))) + (install-file "doc/manual.inc.html" doc))))))) (native-inputs - `(("unzip" ,unzip) ; needed for archive from ftp - ("perl" ,perl) + `(("perl" ,perl) ("pandoc" ,pandoc))) ; for documentation - (home-page "https://ccb.jhu.edu/software/hisat2/index.shtml") + (inputs + `(("python" ,python-wrapper))) + (home-page "https://daehwankimlab.github.io/hisat2/") (synopsis "Graph-based alignment of genomic sequencing reads") (description "HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human -- cgit v1.2.3 From 1a265842e634656411bc7304c4648273f174f65e Mon Sep 17 00:00:00 2001 From: Mark H Weaver Date: Wed, 17 Mar 2021 03:42:12 -0400 Subject: gnu: Use PACKAGE/INHERIT in more places. * gnu/packages/algebra.scm (fftwf, fftw-openmpi), gnu/packages/audio.scm (ztoolkit-rsvg), gnu/packages/bioinformatics.scm (python2-dendropy), gnu/packages/boost.scm (boost-with-python2), gnu/packages/check.scm (python2-mock, python2-pytest-mock), gnu/packages/cups.scm (hplip-minimal), gnu/packages/freedesktop.scm (libinput-minimal), gnu/packages/gettext.scm (gnu-gettext), gnu/packages/glib.scm (python2-pygobject), gnu/packages/gnome.scm (gdl-minimal, libsoup-minimal, python2-pyatspi), gnu/packages/groff.scm (groff-minimal), gnu/packages/jami.scm (ffmpeg-jami), gnu/packages/libcanberra.scm (libcanberra/gtk+-2), gnu/packages/lirc.scm (python2-lirc), gnu/packages/llvm.scm (clang-runtime-3.5), gnu/packages/mpi.scm (java-openmpi, openmpi-thread-multiple), gnu/packages/node.scm (libnode), gnu/packages/onc-rpc.scm (libtirpc/hurd), gnu/packages/python-compression.scm (bitshuffle-for-snappy), gnu/packages/python-crypto.scm (python2-pycrypto, python2-cryptography) (python2-cryptography, python2-m2crypto), gnu/packages/python-web.scm (python2-html2text, python2-tornado) (python2-terminado, python2-ndg-httpsclient, python2-websocket-client) (python2-rauth, python2-url, python2-s3transfer), gnu/packages/python-xyz.scm (python2-psutil, python2-serpent) (python2-humanfriendly, python2-empy, python2-parse-type, python2-polib) (python2-jsonschema, python2-pystache, python2-cython, python2-numpydoc) (python2-ipyparallel, python2-traitlets, python2-dbus) (python2-beautifulsoup4, python2-pep517, python2-flake8, python2-llfuse) (python2-tlsh, python-file, python2-notebook, python-jupyter-console-minimal) (python2-contextlib2, python2-promise, python2-anyjson, python2-amqp) (python2-kombu, python2-billiard, python2-celery, python2-whoosh) (python2-jellyfish, python-rope, ptpython-2, python2-binaryornot) (python2-setproctitle, python2-argcomplete, python2-xopen, python2-isort) (python2-radon, python2-rfc6555, python2-activepapers, python2-send2trash) (python2-cloudpickle, python2-reparser), gnu/packages/python.scm (python2-called-python), gnu/packages/qt.scm (python2-sip, python-pyqt-without-qtwebkit, python2-pyqt) (python-qscintilla, python-pyqt+qscintilla), gnu/packages/scanner.scm (sane-backends), gnu/packages/sdl.scm (guile3.0-sdl2), gnu/packages/selinux.scm (checkpolicy, libselinux, libsemanage, secilc) (python-sepolgen, policycoreutils), gnu/packages/serialization.scm (lua5.1-libmpack, lua5.2-libmpack), gnu/packages/simulation.scm (fenics), gnu/packages/statistics.scm (python2-statsmodels), gnu/packages/texinfo.scm (info-reader), gnu/packages/wxwidgets.scm (wxwidgets-gtk2, wxwidgets-gtk2-3.1), gnu/packages/xml.scm (xmlsec-nss), gnu/packages/xorg.scm (uim-gtk, uim-qt), guix/build-system/python.scm (package-with-explicit-python) (strip-python2-variant): Use PACKAGE/INHERIT. --- gnu/packages/algebra.scm | 4 +- gnu/packages/audio.scm | 3 +- gnu/packages/bioinformatics.scm | 3 +- gnu/packages/boost.scm | 3 +- gnu/packages/check.scm | 4 +- gnu/packages/cups.scm | 3 +- gnu/packages/freedesktop.scm | 2 +- gnu/packages/gettext.scm | 3 +- gnu/packages/glib.scm | 51 ++++++------ gnu/packages/gnome.scm | 9 +- gnu/packages/groff.scm | 3 +- gnu/packages/jami.scm | 3 +- gnu/packages/libcanberra.scm | 2 +- gnu/packages/lirc.scm | 3 +- gnu/packages/llvm.scm | 3 +- gnu/packages/mpi.scm | 5 +- gnu/packages/node.scm | 3 +- gnu/packages/onc-rpc.scm | 8 +- gnu/packages/python-compression.scm | 3 +- gnu/packages/python-crypto.scm | 6 +- gnu/packages/python-web.scm | 20 ++--- gnu/packages/python-xyz.scm | 162 +++++++++++++++--------------------- gnu/packages/python.scm | 3 +- gnu/packages/qt.scm | 10 +-- gnu/packages/scanner.scm | 3 +- gnu/packages/sdl.scm | 3 +- gnu/packages/selinux.scm | 12 +-- gnu/packages/serialization.scm | 4 +- gnu/packages/simulation.scm | 2 +- gnu/packages/statistics.scm | 2 +- gnu/packages/texinfo.scm | 3 +- gnu/packages/wxwidgets.scm | 4 +- gnu/packages/xml.scm | 3 +- gnu/packages/xorg.scm | 6 +- guix/build-system/python.scm | 6 +- 35 files changed, 158 insertions(+), 209 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index d2caa13d0e..129d922751 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -794,7 +794,7 @@ cosine/ sine transforms or DCT/DST).") (license license:gpl2+))) (define-public fftwf - (package (inherit fftw) + (package/inherit fftw (name "fftwf") (arguments (substitute-keyword-arguments (package-arguments fftw) @@ -812,7 +812,7 @@ cosine/ sine transforms or DCT/DST).") " Single-precision version.")))) (define-public fftw-openmpi - (package (inherit fftw) + (package/inherit fftw (name "fftw-openmpi") (inputs `(("openmpi" ,openmpi) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 67a3e57dd9..8b23f04fe5 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -4918,8 +4918,7 @@ edited, converted, compressed and saved.") (license license:lgpl2.1))) (define-public ztoolkit-rsvg - (package - (inherit ztoolkit) + (package/inherit ztoolkit (name "ztoolkit-rsvg") (arguments `(#:configure-flags `("-Denable_rsvg=true"))) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 90e81354a5..eb466868d1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2744,8 +2744,7 @@ trees (phylogenies) and characters.") (define-public python2-dendropy (let ((base (package-with-python2 python-dendropy))) - (package - (inherit base) + (package/inherit base (arguments `(#:phases (modify-phases %standard-phases diff --git a/gnu/packages/boost.scm b/gnu/packages/boost.scm index b1ab8a4ec9..1323e28278 100644 --- a/gnu/packages/boost.scm +++ b/gnu/packages/boost.scm @@ -200,8 +200,7 @@ across a broad spectrum of applications.") "Some components have other similar licences.")))) (define-public boost-with-python2 - (package - (inherit boost) + (package/inherit boost (name "boost-python2") (native-inputs `(("python" ,python-2) diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm index cfda247d67..21514d1bc4 100644 --- a/gnu/packages/check.scm +++ b/gnu/packages/check.scm @@ -836,7 +836,7 @@ have been used.") (define-public python2-mock (let ((base (package-with-python2 (strip-python2-variant python-mock)))) - (package (inherit base) + (package/inherit base (propagated-inputs `(("python2-functools32" ,python2-functools32) ("python2-funcsigs" ,python2-funcsigs) @@ -1240,7 +1240,7 @@ same arguments.") (define-public python2-pytest-mock (let ((base (package-with-python2 (strip-python2-variant python-pytest-mock)))) - (package (inherit base) + (package/inherit base (propagated-inputs `(("python2-mock" ,python2-mock) ,@(package-propagated-inputs base)))))) diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index 2edd5d245c..b18273109e 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -676,8 +676,7 @@ should only be used as part of the Guix cups-pk-helper service.") ("pkg-config" ,pkg-config))))) (define-public hplip-minimal - (package - (inherit hplip) + (package/inherit hplip (name "hplip-minimal") (arguments (substitute-keyword-arguments (package-arguments hplip) diff --git a/gnu/packages/freedesktop.scm b/gnu/packages/freedesktop.scm index e5f9ea71b6..4105dd7ca0 100644 --- a/gnu/packages/freedesktop.scm +++ b/gnu/packages/freedesktop.scm @@ -508,7 +508,7 @@ other applications that need to directly deal with input devices.") (license license:x11))) (define-public libinput-minimal - (package (inherit libinput) + (package/inherit libinput (name "libinput-minimal") (inputs (fold alist-delete (package-inputs libinput) diff --git a/gnu/packages/gettext.scm b/gnu/packages/gettext.scm index bee33f2685..21228694d7 100644 --- a/gnu/packages/gettext.scm +++ b/gnu/packages/gettext.scm @@ -139,8 +139,7 @@ translated messages from the catalogs. Nearly all GNU packages use Gettext.") ;; module when there's a #:renamer, and that module may be empty at that point ;; in case or circular dependencies. (define-public gnu-gettext - (package - (inherit gettext-minimal) + (package/inherit gettext-minimal (name "gettext") (arguments (substitute-keyword-arguments (package-arguments gettext-minimal) diff --git a/gnu/packages/glib.scm b/gnu/packages/glib.scm index 1b9cd71785..5f710a4a38 100644 --- a/gnu/packages/glib.scm +++ b/gnu/packages/glib.scm @@ -833,32 +833,33 @@ useful for C++.") (properties `((python2-variant . ,(delay python2-pygobject)))))) (define-public python2-pygobject - (package (inherit (strip-python2-variant python-pygobject)) - (name "python2-pygobject") + (let ((base (strip-python2-variant python-pygobject))) + (package/inherit base + (name "python2-pygobject") - ;; Note: We use python-build-system here, because Meson only supports - ;; Python 3, and needs PYTHONPATH etc set up correctly, which makes it - ;; difficult to use for Python 2 projects. - (build-system python-build-system) - (arguments - `(#:python ,python-2 - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'delete-broken-tests - (lambda _ - ;; FIXME: this test freezes and times out. - (delete-file "tests/test_mainloop.py") - ;; FIXME: this test fails with this kind of error: - ;; AssertionError: != != Date: Mon, 22 Mar 2021 14:26:13 +0100 Subject: gnu: Add r-signac. * gnu/packages/bioinformatics.scm (r-signac): New variable. Co-authored-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 62 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index eb466868d1..a81c873371 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2020 Pierre Langlois ;;; Copyright © 2020 Bonface Munyoki Kilyungi ;;; Copyright © 2021 Tim Howes +;;; Copyright © 2021 Hong Li ;;; ;;; This file is part of GNU Guix. ;;; @@ -15353,3 +15354,64 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+))) + +(define-public r-signac + (let ((commit "e0512d348adeda4a3f23a2e8f56d1fe09840e03c") + (revision "1")) + (package + (name "r-signac") + (version (git-version "1.1.1" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timoast/signac/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1yihhrv7zs87ax61la1nb4y12lg3knraw4b20k5digbcwm8488lb")))) + (properties `((upstream-name . "Signac"))) + (build-system r-build-system) + (inputs `(("zlib" ,zlib))) + (propagated-inputs + `(("r-annotationfilter" ,r-annotationfilter) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biostrings" ,r-biostrings) + ("r-biovizbase" ,r-biovizbase) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-fastmatch" ,r-fastmatch) + ("r-future" ,r-future) + ("r-future-apply" ,r-future-apply) + ("r-genomeinfodb" ,r-genomeinfodb) + ("r-genomicranges" ,r-genomicranges) + ("r-ggbio" ,r-ggbio) + ("r-ggforce" ,r-ggforce) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-ggseqlogo" ,r-ggseqlogo) + ("r-iranges" ,r-iranges) + ("r-irlba" ,r-irlba) + ("r-lsa" ,r-lsa) + ("r-matrix" ,r-matrix) + ("r-patchwork" ,r-patchwork) + ("r-pbapply" ,r-pbapply) + ("r-rcpp" ,r-rcpp) + ("r-rcpproll" ,r-rcpproll) + ("r-rsamtools" ,r-rsamtools) + ("r-s4vectors" ,r-s4vectors) + ("r-scales" ,r-scales) + ("r-seurat" ,r-seurat) + ("r-seuratobject" ,r-seuratobject) + ("r-stringi" ,r-stringi) + ("r-tidyr" ,r-tidyr))) + (home-page "https://github.com/timoast/signac/") + (synopsis "Analysis of single-cell chromatin data") + (description + "This package provides a framework for the analysis and exploration of +single-cell chromatin data. The Signac package contains functions for +quantifying single-cell chromatin data, computing per-cell quality control +metrics, dimension reduction and normalization, visualization, and DNA +sequence motif analysis.") + (license license:expat)))) -- cgit v1.2.3