From a7a5a994dc7d9307e21e10f842b75ce50065d712 Mon Sep 17 00:00:00 2001
From: pabloaledo <112545720+pabloaledo@users.noreply.github.com>
Date: Wed, 2 Aug 2023 19:22:27 +0200
Subject: [PATCH] bioconductor-dupradar, bioconductor-rsubread: add packages
 (#39206)

* bioconductor-dupradar, bioconductor-rsubread: add packages
* [@spackbot] updating style on behalf of pabloaledo
---
 .../packages/bioconductor-dupradar/package.py | 21 +++++++++++++++++++
 .../packages/bioconductor-rsubread/package.py | 20 ++++++++++++++++++
 2 files changed, 41 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/bioconductor-dupradar/package.py
 create mode 100644 var/spack/repos/builtin/packages/bioconductor-rsubread/package.py

diff --git a/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py
new file mode 100644
index 0000000000..6d7b84ca01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bioconductor-dupradar/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class BioconductorDupradar(RPackage):
+    """Assessment of duplication rates in RNA-Seq datasets"""
+
+    homepage = "https://bioconductor.org/packages/3.16/bioc/html/dupRadar.html"
+    url = "https://bioconductor.org/packages/release/bioc/src/contrib/dupRadar_1.30.0.tar.gz"
+
+    bioc = "dupradar"
+
+    version("1.30.0", sha256="a299d7a4578047dfc19237e34255b0f50f70ce41d29762ef9f5a7741ba35aa3d")
+
+    depends_on("r-kernsmooth")
+    depends_on("subread")
+    depends_on("bioconductor-rsubread")
diff --git a/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py
new file mode 100644
index 0000000000..45428fbe73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bioconductor-rsubread/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class BioconductorRsubread(RPackage):
+    """Mapping, quantification and variant analysis of sequencing data"""
+
+    homepage = "https://bioconductor.org/packages/3.16/bioc/html/Rsubread.html"
+    url = "https://bioconductor.org/packages/release/bioc/src/contrib/Rsubread_2.14.2.tar.gz"
+
+    bioc = "rsubread"
+
+    depends_on("r-matrix")
+    depends_on("zlib")
+
+    version("2.14.2", sha256="ac8be0fad0eb2743443e3a60a9a94eec78c746638aaccca70e7166d034dcebb5")