Changeset 1270:167c1e9c9859
- Timestamp:
- 05/02/08 15:42:59
(8 months ago)
- Author:
- Nate Coraor <nate@bx.psu.edu>
- branch:
- default
- convert_revision:
- svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@2631
- Message:
Remove setup.py, update README.txt
-
Files:
-
Legend:
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| r877 |
r1270 |
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| 1 | | INTRO |
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| 2 | | ===== |
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| | 1 | GALAXY |
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| | 2 | ====== |
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| | 3 | http://g2.bx.psu.edu/ |
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| 3 | 4 | |
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| 4 | | This program requires python 2.4 or later. To check your python version type: |
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| | 5 | The latest information about Galaxy is always available via the Galaxy |
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| | 6 | website above. |
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| 5 | 7 | |
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| 6 | | python -V. |
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| | 8 | HOW TO START |
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| | 9 | ============ |
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| | 10 | Galaxy requires Python 2.4 or 2.5. To check your python version, run: |
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| 7 | 11 | |
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| 8 | | To start a server you need to do run the server as: |
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| | 12 | % python -V |
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| | 13 | Python 2.4.4 |
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| 9 | 14 | |
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| 10 | | python universe.py |
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| | 15 | Before starting Galaxy for the first time, please run the setup script: |
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| 11 | 16 | |
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| 12 | | This will start a server on localhost port 8080. |
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| 13 | | In your browser go to: http://localhost:8080 and you should see the |
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| 14 | | Galaxy environment with some default tools. To customize the tools that |
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| 15 | | are loaded see tool.conf.sample To customize the way your server is ran edit |
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| 16 | | universe.conf |
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| | 17 | % sh setup.sh |
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| 17 | 18 | |
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| 18 | | *Note* certain tools may require certain libraries to be present. |
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| 19 | | (See run.sh for more details) |
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| | 19 | If setup.sh finishes successfully, you can then proceed to starting Galaxy: |
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| 20 | 20 | |
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| | 21 | % sh run.sh |
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| 21 | 22 | |
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| 22 | | RUNTIME ENVIRONMENT |
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| 23 | | =================== |
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| | 23 | Once Galaxy completes startup, you should be able to view Galaxy in your |
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| | 24 | browser at: |
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| 24 | 25 | |
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| 25 | | The default server home will be the directory where the program starts. |
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| 26 | | You can use the UNIVERSE_HOME environment variable to point to a different |
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| 27 | | server home. The path that the UNIVERSE_HOME variable points to must be |
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| 28 | | a directory with the following subdirectories: |
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| | 26 | http://localhost:8080 |
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| 29 | 27 | |
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| 30 | | database |
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| 31 | | database/files |
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| 32 | | database/import |
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| 33 | | tools |
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| | 28 | You may wish to make changes from the default configuration. This can be done |
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| | 29 | in the universe_wsgi.ini file. Tools are configured in tool_conf.xml. Details |
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| | 30 | on adding tools can be found on the Galaxy website (linked above). |
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| 34 | 31 | |
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| 35 | | OPTIMIZED LIBRARIES |
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| 36 | | =================== |
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| | 32 | Not all dependencies are included for the tools provided in the sample |
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| | 33 | tool_conf.xml. A full list of external dependencies is available at: |
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| 37 | 34 | |
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| 38 | | To allow python to load optimized libraries the path to these must be listed |
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| 39 | | in the python path. See the previous section or run.sh for an example. Loading |
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| 40 | | the optimized Cheetah templating libraries can lead to significant |
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| 41 | | performance gains. |
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| 42 | | |
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| 43 | | At startup you the log message: |
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| 44 | | |
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| 45 | | Optimized Namemapper: True|False |
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| 46 | | |
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| 47 | | will tell you whether the optimized Cheetah template was loaded (or not). |
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| 48 | | |
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| 49 | | TOOL DEVELOPMENT |
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| 50 | | ================ |
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| 51 | | |
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| 52 | | See the wiki pages for more details: |
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| 53 | | |
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| 54 | | http://g2.bx.psu.edu |
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| | 35 | http://g2.trac.bx.psu.edu/wiki/ToolDependencies |
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Galaxy