1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7985a6d89435/ Changeset: 7985a6d89435 User: greg Date: 2013-04-16 16:06:41 Summary: Fix for guaranteeing a working directory exists when installing tool dependencies along with tool shed repositories. Bjorn Gruning discovered this issue and submitted pull request # 152 which eliminated the check. The issue was due to checking the file from the python environment instead of hte fabric local environment and ultimately created a package name directory within the Galaxy root directory. This fix will ensure the appropriate directory exists within the fabric local environment. Affected #: 1 file diff -r 64bb99fd3d3cec9a65cc63ecfb0074ac5a87bd93 -r 7985a6d894359c8431e1a9a3a867edc8ff3aefc5 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -91,8 +91,11 @@ # </action> filtered_actions = [ a for a in actions ] dir = install_dir - if not os.path.exists( dir ): - os.makedirs( dir ) + # We need to be careful in determining if the value of dir is a valid directory because we're dealing with 2 environments, the fabric local + # environment and the python environment. Checking the path as follows should work. + full_path_to_dir = os.path.abspath( os.path.join( work_dir, dir ) ) + if not os.path.exists( full_path_to_dir ): + os.makedirs( full_path_to_dir ) # The package has been down-loaded, so we can now perform all of the actions defined for building it. with lcd( dir ): for action_tup in filtered_actions: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.