find-circ: a new package. (#13767)

* find-circ: a new package.

* flake8.

1 files changed, 34 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/find-circ/package.py b/var/spack/repos/builtin/packages/find-circ/package.py
new file mode 100644
index 0000000000..18f6cfb4e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/find-circ/package.py
@@ -0,0 +1,34 @@
+# 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 FindCirc(Package):
+    """Find-circ is a collection of python scripts
+    detecting head-to-tail spliced (back-spliced) sequencing reads,
+    indicative of circular RNA (circRNA) in RNA-seq data."""
+
+    homepage = "https://github.com/marvin-jens/find_circ"
+    url      = "https://github.com/marvin-jens/find_circ/archive/v1.2.tar.gz"
+
+    version('1.2', sha256='f88bf9b5d0cc818313074982d4460c96706f555d924e2821832c3d03bf67743e')
+
+    depends_on('python@2.7:2.8', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    # Higher version of py-pandas and py-numpy
+    # depends on python@3: which conflicts with py-rnacocktail
+    depends_on('py-numpy@:1.16.5', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('cmp_bed.py', prefix.bin)
+        install('find_circ.py', prefix.bin)
+        install('maxlength.py', prefix.bin)
+        install('unmapped2anchors.py', prefix.bin)
+        install('README.md', prefix)
+        install('README.pdf', prefix)
+        install('LICENSE', prefix)
+        install_tree('test_data', prefix.test_data)