py-mixedhtseq: new package at 0.1.0 (#17702)

* py-mixedhtseq: new package at 0.1.0

* py-mixedhtseq: flake8 fixes

1 files changed, 39 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-mixedhtseq/package.py b/var/spack/repos/builtin/packages/py-mixedhtseq/package.py
new file mode 100644
index 0000000000..c01348a099
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mixedhtseq/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2020 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 *
+import glob
+
+
+class PyMixedhtseq(PythonPackage):
+    """HTSeq for mixed single and paired end reads"""
+
+    homepage = "https://github.com/schae234/MixedHTSeq"
+    url      = "https://github.com/schae234/MixedHTSeq/archive/v0.1.0.tar.gz"
+
+    version('0.1.0', sha256='234689c8743ae2ba7ad13bc1809a5248184a4b8d16112d5413e09164ab67e157')
+
+    depends_on('python@2.5:2.8', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-htseq', type=('build', 'run'))
+    depends_on('py-ipython', type=('build', 'run'))
+    depends_on('py-pandas', type=('build', 'run'))
+
+    depends_on('py-setuptools', type='build')
+
+    @run_after('install')
+    def install_scripts(self):
+        shebang = '#!{0}\n'.format(self.spec['python'].command)
+
+        for fname in glob.glob('scripts/*.py'):
+            filter_file('^#!.*', '', fname)
+            with open(fname, 'r') as orig:
+                fdata = orig.read()
+            with open(fname, 'w') as new:
+                new.write(shebang + fdata)
+            set_executable(fname)
+
+        mkdirp(self.prefix.bin)
+        install_tree('scripts', self.prefix.bin)