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: https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
galaxy-dist /
| Filename | Size | Date modified | Message |
|---|---|---|---|
| config | |||
| contrib | |||
| cron | |||
| database | |||
| display_applications | |||
| doc | |||
| external_service_types | |||
| lib | |||
| locale | |||
| openid | |||
| scripts | |||
| static | |||
| templates | |||
| test | |||
| test-data | |||
| tool-data | |||
| tools | |||
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43 B
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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 on the path, coverage report can than be generated with 'coverage html' and viewed at htmlcov/index.html). Update .hgignore to reflect these changes.
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2.0 KB
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Rename ucsc_build_sites.txt to .sample.
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541 B
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Added tag release_2014.04.14 for changeset 9e53251b0b7e
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2.1 KB
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Adding a CITATION file, http://software-carpentry.org/blog/2013/09/introducing-citation-files.html
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10.8 KB
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Reindented license text to make it render better at bitbucket.
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816 B
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updated wiki;
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4.0 KB
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Remove broken and/or obsolete tools.
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60 B
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Allow command-line creation of initial database
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55 B
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First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.
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25.8 KB
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converted tabs to spaces
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1.9 KB
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Add the config for the demo sequencer.
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2.9 KB
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Drop old platforms from dist-eggs.ini.
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521 B
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Object Store: Store the backend object store's ID in the database when using the distributed object store.
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1.8 KB
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Fix old wiki links.
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234 B
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Renamed sequencer to external_service and sequencer_type to external_service_type.
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146 B
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Upgrade of splitting code to do splitting in the tasks versus in the Galaxy process
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5.2 KB
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Fixes for the tool shed's install and test framework.
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9.6 KB
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job_directory -> jobs_directory
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463 B
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Define and implement job destinations, an improved method for defining resources on which Galaxy will run jobs. Functionality is similar to the current system configured via "URLs" in the Galaxy config file, but job concurrency limits on a per-destination basis works (whereas per-URL limits were broken). Sample configs for the new destination system can be found in job_conf.xml.sample_*. Also, renamed ClusterJobRunner to AsynchronousJobRunner, moved worker threads to BaseJobRunner and significantly expanded both of these classes. Updated the tasks, local, lwr, and pbs runners to use destinations, and to inherit from AsynchronousJobRunner, drmaa coming shortly. This should be entirely backwards-compatible, so if you update to this revision and change nothing, your jobs should all still run exactly as they have before. Regardless, it is not recommended that you upgrade your Galaxy instance with jobs running unless you are willing to risk losing those jobs.
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238 B
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Change community to tool_shed in manage_db.sh notes.
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63 B
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File missed in the change set for the re-engineered InstallManager.
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68 B
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The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.
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1.4 KB
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S3/Swift objectstore refactoring.
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220 B
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Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.
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2.0 KB
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Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.
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2.4 KB
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Rename ucsc_build_sites.txt to .sample.
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160 B
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Add a sequencer emulator webapp for demonstration purposes.
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5.5 KB
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Rework workflow functional testing so isn't tested by default...
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153 B
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sample tracking data transfer mechanism streamlined.
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914 B
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Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.
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1.2 KB
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Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.
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849 B
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Add the framework components to enable creating a functional test framework for the tool shed.
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480 B
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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 on the path, coverage report can than be generated with 'coverage html' and viewed at htmlcov/index.html). Update .hgignore to reflect these changes.
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63 B
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Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES
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101 B
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adding setup_rabbitmq.sh script.
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55 B
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First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.
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69 B
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Add new sample config to point to tools installed from a tool shed and add additional directories for checking/creating at startup.
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41 B
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Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly.
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7.1 KB
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Remove migrated tools from main's tool conf.
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9.0 KB
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Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
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3.1 KB
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Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)
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3.0 KB
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Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.
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2.6 KB
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Fix for tool listing with run_functional_tests.sh -list, contributed by Peter Cock.
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3.7 KB
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Fix old wiki links.
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219 B
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Enhance Galaxy tool initialization to do the following:
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36.0 KB
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Remove duplicated enable_unique_workflow_defaults from universe_wsgi.ini.sample.
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