From 6f4dfd90034340f3afbdd921ce0e299697026dfb Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sat, 13 Apr 2024 13:31:35 +0300
Subject: [PATCH] r-spotlight: init

---
 BioArchLinux/r-spotlight/PKGBUILD        | 74 ++++++++++++++++++++++++
 BioArchLinux/r-spotlight/lilac.py        | 14 +++++
 BioArchLinux/r-spotlight/lilac.yaml      | 29 ++++++++++
 BioArchLinux/r-tenxvisiumdata/PKGBUILD   | 36 ++++++++++++
 BioArchLinux/r-tenxvisiumdata/lilac.py   | 14 +++++
 BioArchLinux/r-tenxvisiumdata/lilac.yaml | 13 +++++
 6 files changed, 180 insertions(+)
 create mode 100644 BioArchLinux/r-spotlight/PKGBUILD
 create mode 100644 BioArchLinux/r-spotlight/lilac.py
 create mode 100644 BioArchLinux/r-spotlight/lilac.yaml
 create mode 100644 BioArchLinux/r-tenxvisiumdata/PKGBUILD
 create mode 100644 BioArchLinux/r-tenxvisiumdata/lilac.py
 create mode 100644 BioArchLinux/r-tenxvisiumdata/lilac.yaml

diff --git a/BioArchLinux/r-spotlight/PKGBUILD b/BioArchLinux/r-spotlight/PKGBUILD
new file mode 100644
index 0000000000..65dfc3611e
--- /dev/null
+++ b/BioArchLinux/r-spotlight/PKGBUILD
@@ -0,0 +1,74 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=SPOTlight
+_pkgver=1.6.7
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="\`SPOTlight\`: Spatial Transcriptomics Deconvolution"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-ggplot2
+  r-matrixstats
+  r-nmf
+  r-nnls
+  r-singlecellexperiment
+  r-sparsematrixstats
+)
+checkdepends=(
+  r-dropletutils
+  r-experimenthub
+  r-ggcorrplot
+  r-igraph
+  r-jpeg
+  r-png
+  r-scatterpie
+  r-seuratobject
+  r-spatialexperiment
+  r-tenxvisiumdata
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-colorblindness
+  r-delayedarray
+  r-dropletutils
+  r-experimenthub
+  r-ggcorrplot
+  r-igraph
+  r-jpeg
+  r-knitr
+  r-png
+  r-rmarkdown
+  r-s4vectors
+  r-scater
+  r-scatterpie
+  r-scran
+  r-seurat
+  r-seuratobject
+  r-spatialexperiment
+  r-summarizedexperiment
+  r-tabulamurissenisdata
+  r-tenxvisiumdata
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('0362e0be411e3ed3ce5bf9b928439e10')
+b2sums=('1ea3f06da6af3f44a60c4542032540f72c65304cbce72b1f8132394338ff3d54901989e9bb6027a71a79be292bdcb5252d2dea3ea9a7fa9bddafc8d654828497')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
+}
diff --git a/BioArchLinux/r-spotlight/lilac.py b/BioArchLinux/r-spotlight/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-spotlight/lilac.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-spotlight/lilac.yaml b/BioArchLinux/r-spotlight/lilac.yaml
new file mode 100644
index 0000000000..2935a42bef
--- /dev/null
+++ b/BioArchLinux/r-spotlight/lilac.yaml
@@ -0,0 +1,29 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-ggplot2
+- r-matrixstats
+- r-nmf
+- r-nnls
+- r-singlecellexperiment
+- r-sparsematrixstats
+repo_makedepends:
+- r-dropletutils
+- r-experimenthub
+- r-ggcorrplot
+- r-igraph
+- r-jpeg
+- r-png
+- r-scatterpie
+- r-seuratobject
+- r-spatialexperiment
+- r-tenxvisiumdata
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: SPOTlight
+  repo: bioc
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-tenxvisiumdata/PKGBUILD b/BioArchLinux/r-tenxvisiumdata/PKGBUILD
new file mode 100644
index 0000000000..77165f2f33
--- /dev/null
+++ b/BioArchLinux/r-tenxvisiumdata/PKGBUILD
@@ -0,0 +1,36 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=TENxVisiumData
+_pkgver=1.10.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Visium spatial gene expression data by 10X Genomics"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('MIT')
+depends=(
+  r-experimenthub
+  r-spatialexperiment
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f578add429847efff027a61b1749b9b4')
+b2sums=('99d39e3c83242c776f94cfbcfa2ebff6d96e49827495bbec14aa3952425d3878444ebc5bcdef457ed45c30b021bc460da18742a66bf29121441a3ee9a4080027')
+
+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"
+
+  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-tenxvisiumdata/lilac.py b/BioArchLinux/r-tenxvisiumdata/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-tenxvisiumdata/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-tenxvisiumdata/lilac.yaml b/BioArchLinux/r-tenxvisiumdata/lilac.yaml
new file mode 100644
index 0000000000..384d245ed1
--- /dev/null
+++ b/BioArchLinux/r-tenxvisiumdata/lilac.yaml
@@ -0,0 +1,13 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-experimenthub
+- r-spatialexperiment
+update_on:
+- source: rpkgs
+  pkgname: TENxVisiumData
+  repo: bioc-data-experiment
+  md5: true
+- alias: r