From a54993ad943fad10829e3fa6f446650b4b359ddb Mon Sep 17 00:00:00 2001 From: Pekka Ristola Date: Fri, 12 Apr 2024 20:49:44 +0300 Subject: [PATCH] r-*: add some missing Bioconductor packages --- BioArchLinux/r-metabinr/PKGBUILD | 49 +++++++++++++++++++ BioArchLinux/r-metabinr/lilac.py | 17 +++++++ BioArchLinux/r-metabinr/lilac.yaml | 14 ++++++ BioArchLinux/r-regionalst/PKGBUILD | 58 ++++++++++++++++++++++ BioArchLinux/r-regionalst/lilac.py | 14 ++++++ BioArchLinux/r-regionalst/lilac.yaml | 30 ++++++++++++ BioArchLinux/r-reusedata/PKGBUILD | 39 +++++++++++++++ BioArchLinux/r-reusedata/lilac.py | 14 ++++++ BioArchLinux/r-reusedata/lilac.yaml | 18 +++++++ BioArchLinux/r-scarray.sat/PKGBUILD | 52 ++++++++++++++++++++ BioArchLinux/r-scarray.sat/lilac.py | 14 ++++++ BioArchLinux/r-scarray.sat/lilac.yaml | 23 +++++++++ BioArchLinux/r-simona/PKGBUILD | 70 +++++++++++++++++++++++++++ BioArchLinux/r-simona/lilac.py | 17 +++++++ BioArchLinux/r-simona/lilac.yaml | 27 +++++++++++ 15 files changed, 456 insertions(+) create mode 100644 BioArchLinux/r-metabinr/PKGBUILD create mode 100644 BioArchLinux/r-metabinr/lilac.py create mode 100644 BioArchLinux/r-metabinr/lilac.yaml create mode 100644 BioArchLinux/r-regionalst/PKGBUILD create mode 100644 BioArchLinux/r-regionalst/lilac.py create mode 100644 BioArchLinux/r-regionalst/lilac.yaml create mode 100644 BioArchLinux/r-reusedata/PKGBUILD create mode 100644 BioArchLinux/r-reusedata/lilac.py create mode 100644 BioArchLinux/r-reusedata/lilac.yaml create mode 100644 BioArchLinux/r-scarray.sat/PKGBUILD create mode 100644 BioArchLinux/r-scarray.sat/lilac.py create mode 100644 BioArchLinux/r-scarray.sat/lilac.yaml create mode 100644 BioArchLinux/r-simona/PKGBUILD create mode 100644 BioArchLinux/r-simona/lilac.py create mode 100644 BioArchLinux/r-simona/lilac.yaml diff --git a/BioArchLinux/r-metabinr/PKGBUILD b/BioArchLinux/r-metabinr/PKGBUILD new file mode 100644 index 0000000000..4cc482ade1 --- /dev/null +++ b/BioArchLinux/r-metabinr/PKGBUILD @@ -0,0 +1,49 @@ +# Maintainer: Pekka Ristola + +_pkgname=metabinR +_pkgver=1.4.0 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Abundance and Compositional Based Binning of Metagenomes" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') +depends=( + r-rjava +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocstyle + r-cvms + r-data.table + r-dplyr + r-ggplot2 + r-gridextra + r-knitr + r-r.utils + r-rmarkdown + r-sabre + r-spelling + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('7080ae8eac49640aeae95bda1185ac7d') +b2sums=('aca5dc5305cd8218c5fe4086629d46ad848d9e9a9836dac76e844ba20a2b77e891fb42f1604ec446dbe9cd27615869d7db75e93a9e12536647b0dc5b6dbd92eb') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-metabinr/lilac.py b/BioArchLinux/r-metabinr/lilac.py new file mode 100644 index 0000000000..8d25f04d8e --- /dev/null +++ b/BioArchLinux/r-metabinr/lilac.py @@ -0,0 +1,17 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build( + _G, + expect_systemrequirements = "Java (>= 8)", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-metabinr/lilac.yaml b/BioArchLinux/r-metabinr/lilac.yaml new file mode 100644 index 0000000000..2afbde8f85 --- /dev/null +++ b/BioArchLinux/r-metabinr/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-rjava +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: metabinR + repo: bioc + md5: true +- alias: r diff --git a/BioArchLinux/r-regionalst/PKGBUILD b/BioArchLinux/r-regionalst/PKGBUILD new file mode 100644 index 0000000000..c3b389beda --- /dev/null +++ b/BioArchLinux/r-regionalst/PKGBUILD @@ -0,0 +1,58 @@ +# Maintainer: Pekka Ristola + +_pkgname=RegionalST +_pkgver=1.0.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Investigating regions of interest and performing cross-regional analysis with spatial transcriptomics data" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') +depends=( + r-assertthat + r-bayesspace + r-colorspace + r-dplyr + r-fgsea + r-ggplot2 + r-gridextra + r-magrittr + r-rcolorbrewer + r-s4vectors + r-scater + r-seurat + r-shiny + r-singlecellexperiment + r-summarizedexperiment + r-tibble + r-toast +) +checkdepends=( + r-testthat +) +optdepends=( + r-biocstyle + r-gplots + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('d9589bef7f1408c77dee510baa14b4ad') +b2sums=('82d2fe4733e6bbfc397e0f52e30b13dafd96c5305ac67b8461ceb9edb86c3671d7924b05b441665a1b86c864ae8def6d0687773984f60731a0049132e3257749') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-regionalst/lilac.py b/BioArchLinux/r-regionalst/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-regionalst/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-regionalst/lilac.yaml b/BioArchLinux/r-regionalst/lilac.yaml new file mode 100644 index 0000000000..0625b164af --- /dev/null +++ b/BioArchLinux/r-regionalst/lilac.yaml @@ -0,0 +1,30 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-assertthat +- r-bayesspace +- r-colorspace +- r-dplyr +- r-fgsea +- r-ggplot2 +- r-gridextra +- r-magrittr +- r-rcolorbrewer +- r-s4vectors +- r-scater +- r-seurat +- r-shiny +- r-singlecellexperiment +- r-summarizedexperiment +- r-tibble +- r-toast +repo_makedepends: +- r-testthat +update_on: +- source: rpkgs + pkgname: RegionalST + repo: bioc + md5: true +- alias: r diff --git a/BioArchLinux/r-reusedata/PKGBUILD b/BioArchLinux/r-reusedata/PKGBUILD new file mode 100644 index 0000000000..73fc5210be --- /dev/null +++ b/BioArchLinux/r-reusedata/PKGBUILD @@ -0,0 +1,39 @@ +# Maintainer: Pekka Ristola + +_pkgname=ReUseData +_pkgver=1.2.2 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Reusable and reproducible Data Management" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') +depends=( + r-basilisk + r-biocfilecache + r-jsonlite + r-rcwl + r-rcwlpipelines + r-s4vectors + r-yaml +) +optdepends=( + r-biocstyle + r-knitr + r-rmarkdown + r-testthat +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('c0041ec5d810d0d043c7375e04e78c06') +b2sums=('994e05474d8b9b21045c24b1900055009135f5b5cf8e0d362b15175f719c3cdba80633092cdc9ef8fc26f101cd9f2ef1577560263f7a31727494e43cb330f6d3') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-reusedata/lilac.py b/BioArchLinux/r-reusedata/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-reusedata/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-reusedata/lilac.yaml b/BioArchLinux/r-reusedata/lilac.yaml new file mode 100644 index 0000000000..a5fc4e2446 --- /dev/null +++ b/BioArchLinux/r-reusedata/lilac.yaml @@ -0,0 +1,18 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-basilisk +- r-biocfilecache +- r-jsonlite +- r-rcwl +- r-rcwlpipelines +- r-s4vectors +- r-yaml +update_on: +- source: rpkgs + pkgname: ReUseData + repo: bioc + md5: true +- alias: r diff --git a/BioArchLinux/r-scarray.sat/PKGBUILD b/BioArchLinux/r-scarray.sat/PKGBUILD new file mode 100644 index 0000000000..a4dad2e12f --- /dev/null +++ b/BioArchLinux/r-scarray.sat/PKGBUILD @@ -0,0 +1,52 @@ +# Maintainer: Pekka Ristola + +_pkgname=SCArray.sat +_pkgver=1.2.1 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Large-scale single-cell RNA-seq data analysis using GDS files and Seurat" +arch=(any) +url="https://bioconductor.org/packages/$_pkgname" +license=('GPL-3.0-only') +depends=( + r-biocgenerics + r-biocparallel + r-biocsingular + r-delayedarray + r-gdsfmt + r-s4vectors + r-scarray + r-seurat + r-seuratobject + r-summarizedexperiment +) +checkdepends=( + r-runit +) +optdepends=( + r-biocstyle + r-future + r-knitr + r-markdown + r-rmarkdown + r-runit +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('dfa447cd634a432486a982a719e27451') +b2sums=('c5578e0249789ce5b09ccaf8209b12109f18c68dd37230e2c25259bcbf59eba958d99d56076b0b3d8ac12dcd48e871c0ad16cf7d9ba9933259ee89214823df54') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" Rscript --vanilla runTests.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" +} diff --git a/BioArchLinux/r-scarray.sat/lilac.py b/BioArchLinux/r-scarray.sat/lilac.py new file mode 100644 index 0000000000..b5cdb057c5 --- /dev/null +++ b/BioArchLinux/r-scarray.sat/lilac.py @@ -0,0 +1,14 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build(_G) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-scarray.sat/lilac.yaml b/BioArchLinux/r-scarray.sat/lilac.yaml new file mode 100644 index 0000000000..c0620fb006 --- /dev/null +++ b/BioArchLinux/r-scarray.sat/lilac.yaml @@ -0,0 +1,23 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-biocgenerics +- r-biocparallel +- r-biocsingular +- r-delayedarray +- r-gdsfmt +- r-s4vectors +- r-scarray +- r-seurat +- r-seuratobject +- r-summarizedexperiment +repo_makedepends: +- r-runit +update_on: +- source: rpkgs + pkgname: SCArray.sat + repo: bioc + md5: true +- alias: r diff --git a/BioArchLinux/r-simona/PKGBUILD b/BioArchLinux/r-simona/PKGBUILD new file mode 100644 index 0000000000..aa7951bada --- /dev/null +++ b/BioArchLinux/r-simona/PKGBUILD @@ -0,0 +1,70 @@ +# Maintainer: Pekka Ristola + +_pkgname=simona +_pkgver=1.0.10 +pkgname=r-${_pkgname,,} +pkgver=${_pkgver//-/.} +pkgrel=1 +pkgdesc="Semantic Similarity in Bio-Ontologies" +arch=(x86_64) +url="https://bioconductor.org/packages/$_pkgname" +license=('MIT') +depends=( + java-runtime + perl + r-circlize + r-complexheatmap + r-getoptlong + r-globaloptions + r-igraph + r-matrixstats + r-polychrome + r-rcpp + r-s4vectors + r-shiny + r-xml2 +) +checkdepends=( + r-go.db + r-org.hs.eg.db + r-proxyc + r-testthat +) +optdepends=( + r-annotationdbi + r-annotationhub + r-biocmanager + r-diagrammer + r-go.db + r-interactivecomplexheatmap + r-jsonlite + r-knitr + r-org.hs.eg.db + r-png + r-proxyc + r-ragg + r-simplifyenrichment + r-testthat + r-uniprotkeywords +) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") +md5sums=('3c9d33cfa91dc8e3e071da9fb3bff761') +b2sums=('00f3ed8cce6c401558d4e08365ac82111a00fd7e8f973b438868d58e602efe90b13d528170da13c323d16a4d6eab32ad4445938027834a068ba29c9228656b14') + +build() { + mkdir build + R CMD INSTALL -l build "$_pkgname" +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla test-all.R +} + +package() { + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" + + install -d "$pkgdir/usr/share/licenses/$pkgname" + ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname" +} diff --git a/BioArchLinux/r-simona/lilac.py b/BioArchLinux/r-simona/lilac.py new file mode 100644 index 0000000000..f484b27543 --- /dev/null +++ b/BioArchLinux/r-simona/lilac.py @@ -0,0 +1,17 @@ +#!/usr/bin/env python3 +from lilaclib import * + +import os +import sys +sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions')) +from lilac_r_utils import r_pre_build + +def pre_build(): + r_pre_build( + _G, + expect_systemrequirements = "Perl, Java", + ) + +def post_build(): + git_pkgbuild_commit() + update_aur_repo() diff --git a/BioArchLinux/r-simona/lilac.yaml b/BioArchLinux/r-simona/lilac.yaml new file mode 100644 index 0000000000..b552afae1e --- /dev/null +++ b/BioArchLinux/r-simona/lilac.yaml @@ -0,0 +1,27 @@ +build_prefix: extra-x86_64 +maintainers: +- github: pekkarr + email: pekkarr@protonmail.com +repo_depends: +- r-circlize +- r-complexheatmap +- r-getoptlong +- r-globaloptions +- r-igraph +- r-matrixstats +- r-polychrome +- r-rcpp +- r-s4vectors +- r-shiny +- r-xml2 +repo_makedepends: +- r-go.db +- r-org.hs.eg.db +- r-proxyc +- r-testthat +update_on: +- source: rpkgs + pkgname: simona + repo: bioc + md5: true +- alias: r