From 969a634a0ee776da28eebe0f22d4f89ebf79460d Mon Sep 17 00:00:00 2001 From: Chris Tomkins-Tinch Date: Tue, 4 Dec 2018 20:10:30 -0500 Subject: [PATCH] add fallback method for bioconda wrapper of gatk v3 (#902) 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. --- tools/gatk.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tools/gatk.py b/tools/gatk.py index 799836bd5..34c462c1f 100644 --- a/tools/gatk.py +++ b/tools/gatk.py @@ -44,6 +44,7 @@ def __init__(self, path=None): ) ) 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