2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/77e5cbd3bcfe/ Changeset: 77e5cbd3bcfe User: jmchilton Date: 2014-01-14 23:02:11 Summary: Fix R env handling in fabric_util broken with 864f8f4. Thanks BjoernGruening. Affected #: 1 file diff -r 027eb5827babc5a6b07b6c3e098bacd09185adf4 -r 77e5cbd3bcfebf50ce463c0b320a51e288f00a1e 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 @@ -409,7 +409,7 @@ with lcd( current_dir ): with settings( warn_only=True ): for tarball_name in tarball_names: - cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; && + cmd = '''PATH=$PATH:$R_HOME/bin; export PATH; R_LIBS=$INSTALL_DIR; export R_LIBS; Rscript -e "install.packages(c('%s'),lib='$INSTALL_DIR', repos=NULL, dependencies=FALSE)"''' % ( str( tarball_name ) ) cmd = install_environment.build_command( td_common_util.evaluate_template( cmd, install_dir ) ) return_code = handle_command( app, tool_dependency, install_dir, cmd ) https://bitbucket.org/galaxy/galaxy-central/commits/55a2d1cced87/ Changeset: 55a2d1cced87 User: jmchilton Date: 2014-01-14 23:05:01 Summary: Merge latest. Affected #: 1 file diff -r 77e5cbd3bcfebf50ce463c0b320a51e288f00a1e -r 55a2d1cced87aa2401a99ff3bc33d759f9b6e82c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -497,9 +497,10 @@ suc.repository_was_previously_installed( trans, tool_shed_url, name, tmp_repo_info_tuple ) if installed_repository: current_changeset_revision = str( installed_repository.changeset_revision ) - message = 'Revision %s of repository %s owned by %s has already been installed.' + message = 'Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed.' % \ + ( latest_downloadable_revision, name, owner ) if current_changeset_revision != latest_downloadable_revision: - message += ' The current changeset revision is %s.' % current_changeset_revision + message += ' The current changeset revision is <b>%s</b>.' % current_changeset_revision status = 'error' else: # Install the latest downloadable revision of the repository. @@ -508,10 +509,10 @@ ( name, owner, latest_downloadable_revision, web.url_for( '/', qualified=True ) ) ) return trans.response.send_redirect( url ) else: - message = 'Cannot locate installed tool shed repository with encoded id %s.' % str( repository_id ) + message = 'Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str( repository_id ) status = 'error' else: - message = 'The request parameters did not include the required encoded id of installed repository.' + message = 'The request parameters did not include the required encoded <b>id</b> of installed repository.' status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', 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.