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James Taylor
7bfc238304
#) An "xy_plot" tool and a new "build_ucsc_custom_track" tool that
demonstrate the various features added here.
#) Grouping constructs for tool parameters:
- "repeat" element allows for a set of parameters to be repeated an
arbitrary number of times
- "conditional" element allows choosing a set of parameters to display
based on the value of another parameter
These constructs can be arbitrarily nested. Their values are structured
and can be used in hooks, validation, et cetera
#) Support for generating arbitrary config files to pass to a tool
#) Command lines are now full Cheetah templates
#) Better job error reporting, includes tracebacks for internal errors
preparing the job (database change required, see below!)
#) Preparation of command line, config files, exec_before_job hook moved
into job execution stage
#) Parameter values now jsonified before storing in database (this is much
more rigorous that before, and restoring from the database now works
properly)
DATABASE CHANGE:
alter table job add column traceback text;
INTRO ===== This program requires python 2.4 or later. To check your python version type: python -V. To start a server you need to do run the server as: python universe.py This will start a server on localhost port 8080. In your browser go to: http://localhost:8080 and you should see the Galaxy environment with some default tools. To customize the tools that are loaded see tool.conf.sample To customize the way your server is ran edit universe.conf *Note* certain tools may require certain libraries to be present. (See run.sh for more details) RUNTIME ENVIRONMENT =================== The default server home will be the directory where the program starts. You can use the UNIVERSE_HOME environment variable to point to a different server home. The path that the UNIVERSE_HOME variable points to must be a directory with the following subdirectories: database database/files database/import tools OPTIMIZED LIBRARIES =================== To allow python to load optimized libraries the path to these must be listed in the python path. See the previous section or run.sh for an example. Loading the optimized Cheetah templating libraries can lead to significant performance gains. At startup you the log message: Optimized Namemapper: True|False will tell you whether the optimized Cheetah template was loaded (or not). The log message: database type: dbhash|.... will tell you what kind of underlying database is the server using. Dbhash stands for the BerkleyDB. The server should work fine with other libraries as well but BerkleyDB is provides the most reliable and efficient storage. TOOL DEVELOPMENT ================ See the wiki pages for more details: http://g2.bx.psu.edu CREATING A RELEASE ================== type: python setup.py sdist