r-hicontacts: init

BioArchLinux/r-bsgenome.scerevisiae.ucsc.saccer3/PKGBUILD

@@ -0,0 +1,27 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=BSgenome.Scerevisiae.UCSC.sacCer3
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer3)"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(Artistic2.0)
+depends=(
+  r-bsgenome
+)
+source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('7f2d8bba69c3dcebf426d9b19a6bed30')
+sha256sums=('b543b39508958a21fa4bf1b73f934332c737c6a6190edcb71d8178d7491acdde')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-bsgenome.scerevisiae.ucsc.saccer3/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_needscompilation = "",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-bsgenome.scerevisiae.ucsc.saccer3/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-bsgenome
+update_on:
+- source: rpkgs
+  pkgname: BSgenome.Scerevisiae.UCSC.sacCer3
+  repo: bioc-data-annotation
+  md5: true
+- alias: r

BioArchLinux/r-hicontacts/PKGBUILD

@@ -0,0 +1,75 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=HiContacts
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Analysing cool files in R with HiContacts"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-biocgenerics
+  r-biocio
+  r-biocparallel
+  r-dplyr
+  r-genomeinfodb
+  r-genomicranges
+  r-ggplot2
+  r-ggrastr
+  r-hicexperiment
+  r-interactionset
+  r-iranges
+  r-readr
+  r-rspectra
+  r-s4vectors
+  r-scales
+  r-stringr
+  r-summarizedexperiment
+  r-tibble
+  r-tidyr
+)
+checkdepends=(
+  r-bsgenome.scerevisiae.ucsc.saccer3
+  r-hicontactsdata
+  r-rfast
+  r-testthat
+  r-wgcna
+)
+optdepends=(
+  r-biocstyle
+  r-biostrings
+  r-bsgenome.scerevisiae.ucsc.saccer3
+  r-genomicfeatures
+  r-hicontactsdata
+  r-knitr
+  r-patchwork
+  r-rfast
+  r-rmarkdown
+  r-rtracklayer
+  r-terra
+  r-testthat
+  r-wgcna
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f7f7341e5b4cbfcd13b04fadd9c472c7')
+sha256sums=('7efd2cc7f77c82fe4e2b662fc54f093d68ee045c4d89c0f2400a4409bcf5ab29')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+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" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-hicontacts/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()

BioArchLinux/r-hicontacts/lilac.yaml

@@ -0,0 +1,36 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocgenerics
+- r-biocio
+- r-biocparallel
+- r-dplyr
+- r-genomeinfodb
+- r-genomicranges
+- r-ggplot2
+- r-ggrastr
+- r-hicexperiment
+- r-interactionset
+- r-iranges
+- r-readr
+- r-rspectra
+- r-s4vectors
+- r-scales
+- r-stringr
+- r-summarizedexperiment
+- r-tibble
+- r-tidyr
+repo_makedepends:
+- r-bsgenome.scerevisiae.ucsc.saccer3
+- r-hicontactsdata
+- r-rfast
+- r-testthat
+- r-wgcna
+update_on:
+- source: rpkgs
+  pkgname: HiContacts
+  repo: bioc
+  md5: true
+- alias: r