From b5e7979b04333c7786c487bebc16ccc1427ed570 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Fri, 12 Apr 2024 18:37:38 +0300
Subject: [PATCH] r-genproseq: init

---
 BioArchLinux/r-genproseq/PKGBUILD   | 50 +++++++++++++++++++++++++++++
 BioArchLinux/r-genproseq/lilac.py   | 14 ++++++++
 BioArchLinux/r-genproseq/lilac.yaml | 21 ++++++++++++
 BioArchLinux/r-word2vec/PKGBUILD    | 33 +++++++++++++++++++
 BioArchLinux/r-word2vec/lilac.py    | 14 ++++++++
 BioArchLinux/r-word2vec/lilac.yaml  | 14 ++++++++
 6 files changed, 146 insertions(+)
 create mode 100644 BioArchLinux/r-genproseq/PKGBUILD
 create mode 100644 BioArchLinux/r-genproseq/lilac.py
 create mode 100644 BioArchLinux/r-genproseq/lilac.yaml
 create mode 100644 BioArchLinux/r-word2vec/PKGBUILD
 create mode 100644 BioArchLinux/r-word2vec/lilac.py
 create mode 100644 BioArchLinux/r-word2vec/lilac.yaml

diff --git a/BioArchLinux/r-genproseq/PKGBUILD b/BioArchLinux/r-genproseq/PKGBUILD
new file mode 100644
index 0000000000..3a9909e6dc
--- /dev/null
+++ b/BioArchLinux/r-genproseq/PKGBUILD
@@ -0,0 +1,50 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=GenProSeq
+_pkgver=1.6.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Generating Protein Sequences with Deep Generative Models"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
+depends=(
+  r-catencoders
+  r-deeppincs
+  r-keras
+  r-mclust
+  r-reticulate
+  r-tensorflow
+  r-ttgsea
+  r-word2vec
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-ggseqlogo
+  r-knitr
+  r-rmarkdown
+  r-stringdist
+  r-testthat
+  r-vaexprs
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('15e772912f2019256df52d192edd5402')
+b2sums=('b8a9e9720d3008a3c655ca8b3917ec5f23da709e39a69e47cb3c2f87bb1c0f01a65bc3b62777ae2226cf5d506fa75cb2eed0a45519e8a33ce4d0f964adbb22af')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_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" "$pkgdir/usr/lib/R/library"
+}
diff --git a/BioArchLinux/r-genproseq/lilac.py b/BioArchLinux/r-genproseq/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-genproseq/lilac.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-genproseq/lilac.yaml b/BioArchLinux/r-genproseq/lilac.yaml
new file mode 100644
index 0000000000..c64b8e2850
--- /dev/null
+++ b/BioArchLinux/r-genproseq/lilac.yaml
@@ -0,0 +1,21 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-catencoders
+- r-deeppincs
+- r-keras
+- r-mclust
+- r-reticulate
+- r-tensorflow
+- r-ttgsea
+- r-word2vec
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: GenProSeq
+  repo: bioc
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-word2vec/PKGBUILD b/BioArchLinux/r-word2vec/PKGBUILD
new file mode 100644
index 0000000000..b426b44661
--- /dev/null
+++ b/BioArchLinux/r-word2vec/PKGBUILD
@@ -0,0 +1,33 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=word2vec
+_pkgver=0.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Distributed Representations of Words"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=(Apache)
+depends=(
+  r-rcpp
+)
+makedepends=(
+  r-rcppprogress
+)
+optdepends=(
+  r-udpipe
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('2fa2b87d0b3041086da4fd50135cbc4a')
+b2sums=('536a341372cda93dd75509ca1e8bd5a1de9654f489ad30ffab9890fc92f3798144e01c2825c9824d09f45eaba3716ca1807b31205c8376b57a0ee44951bdb8ad')
+
+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-word2vec/lilac.py b/BioArchLinux/r-word2vec/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-word2vec/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-word2vec/lilac.yaml b/BioArchLinux/r-word2vec/lilac.yaml
new file mode 100644
index 0000000000..f4a987c231
--- /dev/null
+++ b/BioArchLinux/r-word2vec/lilac.yaml
@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-rcpp
+repo_makedepends:
+- r-rcppprogress
+update_on:
+- source: rpkgs
+  pkgname: word2vec
+  repo: cran
+  md5: true
+- alias: r