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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
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Remove setup.py, update README.txt

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  • README.txt

    r877 r1270  
    1 INTRO 
    2 ===== 
     1GALAXY 
     2====== 
     3http://g2.bx.psu.edu/ 
    34 
    4 This program requires python 2.4 or later. To check your python version type: 
     5The latest information about Galaxy is always available via the Galaxy 
     6website above. 
    57 
    6 python -V. 
     8HOW TO START 
     9============ 
     10Galaxy requires Python 2.4 or 2.5. To check your python version, run: 
    711 
    8 To start a server you need to do run the server as: 
     12% python -V 
     13Python 2.4.4 
    914 
    10 python universe.py 
     15Before starting Galaxy for the first time, please run the setup script: 
    1116 
    12 This will start a server on localhost port 8080.  
    13 In your browser go to: http://localhost:8080 and you should see the  
    14 Galaxy environment with some default tools. To customize the tools that  
    15 are loaded see tool.conf.sample To customize the way your server is ran edit  
    16 universe.conf  
     17% sh setup.sh 
    1718 
    18 *Note* certain tools may require certain libraries to be present. 
    19 (See run.sh for more details) 
     19If setup.sh finishes successfully, you can then proceed to starting Galaxy: 
    2020 
     21% sh run.sh 
    2122 
    22 RUNTIME ENVIRONMENT 
    23 =================== 
     23Once Galaxy completes startup, you should be able to view Galaxy in your 
     24browser at: 
    2425 
    25 The default server home will be the directory where the program starts. 
    26 You can use the UNIVERSE_HOME environment variable to point to a different 
    27 server home. The path that the UNIVERSE_HOME variable points to must be  
    28 a directory with the following subdirectories: 
     26http://localhost:8080 
    2927 
    30 database 
    31 database/files 
    32 database/import 
    33 tools 
     28You may wish to make changes from the default configuration.  This can be done 
     29in the universe_wsgi.ini file.  Tools are configured in tool_conf.xml.  Details 
     30on adding tools can be found on the Galaxy website (linked above). 
    3431 
    35 OPTIMIZED LIBRARIES 
    36 =================== 
     32Not all dependencies are included for the tools provided in the sample 
     33tool_conf.xml.  A full list of external dependencies is available at: 
    3734 
    38 To allow python to load optimized libraries the path to these must be listed  
    39 in the python path. See the previous section or run.sh for an example. Loading  
    40 the optimized Cheetah templating libraries can lead to significant  
    41 performance gains.  
    42  
    43 At startup you the log message:  
    44  
    45 Optimized  Namemapper: True|False 
    46  
    47 will tell you whether the optimized Cheetah template was loaded (or not). 
    48  
    49 TOOL DEVELOPMENT 
    50 ================ 
    51  
    52 See the wiki pages for more details: 
    53  
    54 http://g2.bx.psu.edu 
     35http://g2.trac.bx.psu.edu/wiki/ToolDependencies