From 01b2a9944ce66114eab7856e30ccdee63cb2d82b Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sat, 21 Oct 2023 11:00:03 +0300
Subject: [PATCH] r-msa2dist: init, dependency of r-doubletrouble

---
 BioArchLinux/r-msa2dist/PKGBUILD   | 59 ++++++++++++++++++++++++++++++
 BioArchLinux/r-msa2dist/lilac.py   | 18 +++++++++
 BioArchLinux/r-msa2dist/lilac.yaml | 28 ++++++++++++++
 3 files changed, 105 insertions(+)
 create mode 100644 BioArchLinux/r-msa2dist/PKGBUILD
 create mode 100644 BioArchLinux/r-msa2dist/lilac.py
 create mode 100644 BioArchLinux/r-msa2dist/lilac.yaml

diff --git a/BioArchLinux/r-msa2dist/PKGBUILD b/BioArchLinux/r-msa2dist/PKGBUILD
new file mode 100644
index 0000000000..12e34c8321
--- /dev/null
+++ b/BioArchLinux/r-msa2dist/PKGBUILD
@@ -0,0 +1,59 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=MSA2dist
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-ape
+  r-biostrings
+  r-doparallel
+  r-dplyr
+  r-foreach
+  r-genomicranges
+  r-iranges
+  r-rcpp
+  r-rlang
+  r-seqinr
+  r-stringi
+  r-stringr
+  r-tibble
+  r-tidyr
+)
+makedepends=(
+  r-rcppthread
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-devtools
+  r-ggplot2
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('69cf471088b61e2f4ce253992ace214a')
+sha256sums=('b2b9f16739172d99e9a90e379716cd5ad9a4e286059557ac8e0ea64cdfbfdad8')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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"
+}
diff --git a/BioArchLinux/r-msa2dist/lilac.py b/BioArchLinux/r-msa2dist/lilac.py
new file mode 100644
index 0000000000..7f509ece89
--- /dev/null
+++ b/BioArchLinux/r-msa2dist/lilac.py
@@ -0,0 +1,18 @@
+#!/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_license = "GPL-3 + file LICENSE",
+        expect_systemrequirements = "C++11",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-msa2dist/lilac.yaml b/BioArchLinux/r-msa2dist/lilac.yaml
new file mode 100644
index 0000000000..f00e84ac44
--- /dev/null
+++ b/BioArchLinux/r-msa2dist/lilac.yaml
@@ -0,0 +1,28 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-ape
+- r-biostrings
+- r-doparallel
+- r-dplyr
+- r-foreach
+- r-genomicranges
+- r-iranges
+- r-rcpp
+- r-rlang
+- r-seqinr
+- r-stringi
+- r-stringr
+- r-tibble
+- r-tidyr
+repo_makedepends:
+- r-rcppthread
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: MSA2dist
+  repo: bioc
+  md5: true
+- alias: r