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add fallback method for bioconda wrapper of gatk v3 (#902)
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add install method for `gatk` executable as well as `gatk3` as provided by bioconda.  The current [recipe](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/gatk/build.sh) uses gatk3, however a new install received a package build with the older `gatk` executable name (some bioconda packages are currently in build flux). This adds a fallback method so either executable supplied by bioconda will work.
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tomkinsc committed Dec 5, 2018
1 parent 3cf1208 commit 969a634
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Expand Up @@ -44,6 +44,7 @@ def __init__(self, path=None):
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install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable="gatk3"))
install_methods.append(tools.CondaPackage(TOOL_NAME, version=TOOL_VERSION, executable="gatk"))
tools.Tool.__init__(self, install_methods=install_methods)

def execute(self, command, gatkOptions=None, JVMmemory=None): # pylint: disable=W0221
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