2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4294c2a836fe/ Changeset: 4294c2a836fe User: jmchilton Date: 2013-05-26 22:15:19 Summary: Fix job splitting to rewrite references in config files in addition to command-line. Affected #: 1 file diff -r 31714646a7b441f34a43748065278a1b08940c3c -r 4294c2a836fea78d50e65c29fc85bb047b095fd3 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1573,6 +1573,12 @@ self.sa_session.flush() # Build any required config files config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) + for config_filename in config_filenames: + config_contents = open(config_filename, "r").read() + for k, v in fnames.iteritems(): + config_contents = config_contents.replace(k, v) + open(config_filename, "w").write(config_contents) + # FIXME: Build the param file (might return None, DEPRECATED) param_filename = self.tool.build_param_file( param_dict, self.working_directory ) # Build the job's command line https://bitbucket.org/galaxy/galaxy-central/commits/f3e6cf36517e/ Changeset: f3e6cf36517e User: dannon Date: 2013-05-28 20:43:12 Summary: Merged in jmchilton/galaxy-central-api-history-uploads (pull request #169) Fix job splitting to rewrite references in config files in addition to command-line. Affected #: 1 file diff -r a3f91ab1dc83c242ef284627df58f19ee95c0b12 -r f3e6cf36517e7db7b507fc1b15af7a43ad4a84f5 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1573,6 +1573,12 @@ self.sa_session.flush() # Build any required config files config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) + for config_filename in config_filenames: + config_contents = open(config_filename, "r").read() + for k, v in fnames.iteritems(): + config_contents = config_contents.replace(k, v) + open(config_filename, "w").write(config_contents) + # FIXME: Build the param file (might return None, DEPRECATED) param_filename = self.tool.build_param_file( param_dict, self.working_directory ) # Build the job's command line 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.