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Daniel Blankenberg
f39f4d4694
From Cathy: I have posted an updated version of Laj, which exits with an error message if there is an integer overflow in building the composite y-axis for the dotplot (overflows for individual sequences would already be caught by the parser). I ran it on your file, and indeed that was the problem.
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. We have included a binary copy of galaxyOps for linux systems. (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