rnaquast: add new package (#22648)

1 files changed, 37 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/rnaquast/package.py b/var/spack/repos/builtin/packages/rnaquast/package.py
new file mode 100644
index 0000000000..8ffc85a26c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rnaquast/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2021 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)
+
+import os
+from spack import *
+
+
+class Rnaquast(Package):
+    """Quality assessment of de novo transcriptome assemblies from RNA-Seq data
+
+    rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome
+    and gene database. In addition, rnaQUAST is also capable of estimating gene
+    database coverage by raw reads and de novo quality assessment
+    using third-party software."""
+
+    homepage = "https://github.com/ablab/rnaquast"
+    url      = "https://github.com/ablab/rnaquast/archive/refs/tags/v2.2.0.tar.gz"
+
+    maintainers = ['dorton21']
+
+    version('2.2.0', sha256='117dff9d9c382ba74b7b0ff24bc7b95b9ca6aa701ebf8afd22943aa54e382334')
+
+    depends_on('python@2.5:', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-joblib', type=('build', 'run'))
+    depends_on('py-gffutils', type=('build', 'run'))
+    depends_on('gmap-gsnap', type=('build', 'run'))
+    depends_on('blast-plus', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
+        os.rename('%s/rnaQUAST.py' % prefix.bin, '%s/rnaQUAST' % prefix.bin)
+
+    def setup_run_environment(self, env):
+        env.prepend_path('PATH', prefix.bin)