py-atropos: new package (#12745)

* create new package py-atropos

* remove whitespace

* make tqdm and pysam dependencies optional, exposed as variants

1 files changed, 26 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-atropos/package.py b/var/spack/repos/builtin/packages/py-atropos/package.py
new file mode 100644
index 0000000000..2e92394a75
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-atropos/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2019 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 import *
+
+
+class PyAtropos(PythonPackage):
+    """Atropos is tool for specific, sensitive, and speedy trimming of NGS
+    reads. It is a fork of the venerable Cutadapt read trimmer."""
+
+    homepage = "https://atropos.readthedocs.io"
+    url      = "https://pypi.io/packages/source/a/atropos/atropos-1.1.22.tar.gz"
+    git      = "https://github.com/jdidion/atropos.git"
+
+    version('1.1.22', sha256='05e40cb9337421479c692e1154b962fbf811d7939b72c197a024929b7ae88b78')
+
+    depends_on('python@3.3:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-cython@0.25.2:', type='build')
+    depends_on('py-tqdm', type=('build', 'run'), when='+tqdm')
+    depends_on('py-pysam', type=('build', 'run'), when='+pysam')
+
+    variant('tqdm', default=False, description='Enable progress bar')
+    variant('pysam', default=False, description='Enable bam file parsing')