1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/8fb2a905f249/ changeset: 8fb2a905f249 user: greg date: 2012-11-06 21:09:34 summary: Per James Johnson, allow for environment variables that contain neither REPOSITORY_INSTALL_DIR nor INSTALL_DIR when defining tool dependencies to be installed along with tool shed repositories. affected #: 1 file

diff -r 3d27b35e1c1fa629ec4175f5e613b5a771152377 -r 8fb2a905f2492a388799ac4d861e52bda9365300 lib/galaxy/tool_shed/tool_dependencies/common_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py @@ -19,6 +19,14 @@ else: env_var_text = elem.text.replace( '$INSTALL_DIR', tool_shed_repository_install_dir ) return dict( name=env_var_name, action=env_var_action, value=env_var_text ) + if elem.text: + # Allow for environment variables that contain neither REPOSITORY_INSTALL_DIR nor INSTALL_DIR since there may be command line + # parameters that are tuned for a Galaxy instance. Allowing them to be set in one location rather than being hard coded into + # each tool config is the best approach. For example: + # <environment_variable name="GATK2_SITE_OPTIONS" action="set_to"> + # "--num_threads 4 --num_cpu_threads_per_data_thread 3 --phone_home STANDARD" + # </environment_variable> + return dict( name=env_var_name, action=env_var_action, value=elem.text) return None def create_or_update_env_shell_file( install_dir, env_var_dict ): env_var_name = env_var_dict[ 'name' ]

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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