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GALAXY ====== http://galaxyproject.org/ The latest information about Galaxy is always available via the Galaxy website above. HOW TO START ============ Galaxy requires Python 2.6 or 2.7. To check your python version, run: % python -V Python 2.7.3 Start Galaxy: % sh run.sh Once Galaxy completes startup, you should be able to view Galaxy in your browser at: http://localhost:8080 You may wish to make changes from the default configuration. This can be done in the universe_wsgi.ini file. Tools are configured in tool_conf.xml. Details on adding tools can be found on the Galaxy website (linked above). Not all dependencies are included for the tools provided in the sample tool_conf.xml. A full list of external dependencies is available at: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
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Commit commented on in jmchilton/galaxy-central-multi-input-tool-fixes-2
e001605 Fix bug related to trailing semi-colon in tools.
6fdf96b Refactor building command lines out of job runner base into its own module.
829c047 Force odict usage (sorted by 'order' key in object_store_config) for HierarchicalObjectStore
750e687 Create an HDA delete method for the history contents API.
3e27794 Add pause option to new upload front end
312c565 Improved handling of tools printing unicode output.
ec5e78d Improved handling of tools producing unicode output.
c78f3f6 Refactor job status checking logic into its own module.
ba45d14 user activation flow tweaked, link at the masthead message providing activation resending
9b73897 Fix stdio return code handling that has been broken for a few releases.
f45445c Correct documentation for path used to perform tool shed API-based installs.
373ae15 Eliminate dependency on git and bash for CloudBioLinux tool shed package installer, use new sh based deployer script in CBL and download tars instead of ...
8000822 Implement 'cloudbiolinux_install' tool shed package install action.
62cd8fb Fix rvm tool infrastructure for case when tool_dependency_dir is a relative path. Thanks to @iracooke for the bug report.
522e26e Implement high-level Galaxy tool shed install option for creating isolated Ruby environments using RVM.
50eb1ee Setup abstraction (InstallEnvrionment) in tool shed client for capturing the environment setup to during building and installations of packages. This simplifies install_and_build_package and provides a ...
1dd103d Implement 'cloudbiolinux_install' tool shed package install action.
f33c054 Fix for the download_binary action type incorrectly processing downloaded compressed files.
773941f Automated merge of next-stable branch
3615504 Update citation for Tophat2.
48220b0 Visualizations framework: fix to_param optionality bug, add has_dataprovider data source test
cf53a00 Slight simplification of logic related to implementation of tool.requires_login.
1dd1b4a Fix tool.requires_login behvaior broken with dynamic tool box filters (sorry again Dan and thanks for the bug report).
4a514b0 When deleting histories, go to default history (unnamed, no datasets) if available and create new history only if necessary.
2a5554c Merge next-stable.
9e57b3a Bugfix for stopping jobs with the PBS plugin.
20e2d05 Tophat2 wrapper enhancements: (a) better error handling; (b) include alignment statistics in output; and (c) document compatible tool versions.
71bd004 Update README.txt to reflect Python 2.5 is no longer supported.
682bc70 Create unit test directory with example test. Enable coverage report generation of unit tests (run_unit_tests.sh will automatically add --with-coverage to nosetests call if coverage is ...
dc6e034 Enhance the Galaxy API for installing tool shed repositories to make sure the tool_dependency_dir setting is defined in the Galaxy configuration file if installing tool ...
acc4a22 Add the threadpool_kill_thread_limit setting to the tool shed's sample configuration file.
4f7b7e4 Add more package requirements for datatype converters
3636ba2 Add config option 'welcome_url' to allow override of relative url to welcome file. Much like the tool filter request, the driving motivation here is allowing ...
d794e30 Refactor hardcoded references to static/welcome.html to a new welcome action on the root controller.
68c705b Fix toolshed migration 0017 to work with both postgres, postgresql dialect names
30e8f84 Fix toolshed migration 0017 to work with both postgres, postgresql dialect names
827ff13 Condor runner: Allow for per-destination ClassAd query params, don't delete the submit file if submission fails and cleanup_job != always.