Merge branch 'master' into ct-broad_uger_runtime_changes

README.md

@@ -1,4 +1,4 @@
-[![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](https://bioconda.github.io/recipes/viral-ngs/README.html)
+[![broad-viral-badge](https://img.shields.io/badge/install%20from-broad--viral-green.svg?style=flat-square)](https://anaconda.org/broad-viral/viral-ngs)
 [![Build Status](https://travis-ci.org/broadinstitute/viral-ngs.svg?branch=master)](https://travis-ci.org/broadinstitute/viral-ngs)
 [![Coverage Status](https://coveralls.io/repos/broadinstitute/viral-ngs/badge.png)](https://coveralls.io/r/broadinstitute/viral-ngs)
 [![Code Health](https://landscape.io/github/broadinstitute/viral-ngs/master/landscape.svg?style=flat)](https://landscape.io/github/broadinstitute/viral-ngs)

docs/conf.py

@@ -25,7 +25,7 @@
 import mock
 MOCK_MODULES = ['scipy', 'pysam', 'Bio', 'Bio.AlignIO', 'Bio.Alphabet',
                 'Bio.Alphabet.IUPAC', 'Bio.SeqIO', 'Bio.Data.IUPACData',
-		'pybedtools', 'pybedtools.BedTool']
+		        'Bio.Seq', 'pybedtools', 'pybedtools.BedTool']
 for mod_name in MOCK_MODULES:
     sys.modules[mod_name] = mock.Mock()
 

requirements-py-docs.txt

@@ -2,3 +2,4 @@ Sphinx==1.4.4
 sphinx-argparse==0.1.15
 sphinx_rtd_theme==0.1.9
 matplotlib==1.5.3
+PyYAML==3.11