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0README
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0README
For xGDBvm, a virtual environment for genome annotation
Updated: 2-3-2016 J Duvick
/xGDBvm is the document root directory which includes:
0README- this file
0README-iPlant - instructions specific to the iPlant implementation of xGDBvm
admin - directory of administrative scripts for online operation
dist.htaccess - template for .htaccess file if this directory level is password-protected
data -> /home/xgdb-data - symlink to directory used for GDB ouptput data -- on iPlant, typically mounted to block storage volume
dist.htacces - can be converted to .htaccess for password protection of top level
examples - directory of example data for creating test GDB
favicon.ico - browser window icon
index.php - top page
input -> /home/xgdb-input (symlink to directory for user's input data -- on iPlant, typically mounted to user's Data Store
LICENSE - GPL license for this software
README.md - used by github to summarize the project
robots.txt - configured to exclude crawling
scratch -> /xGDBvm/data/scratch symlink to temporary directory for pipeline calculations
scripts - directory of off line process pipelines and templates as well as gdb data processes like parser, loading scripts
src - source code for BLAST, GeneSeqer, GAEVAL; as well as yrGATE code and Web scripts
tmp -> /xGDBvm/data/tmp (symlink to directory for temporary files cached during page display
XGDB - directory of core xGDB modules including Perl, Perl cgi and PHP scripts, Perl and PHP configuration scripts, images, css resources
Startup Instructions:
If this is an iPlant (CyVerse) instance, type 'quickstart' or 'instructions' and follow instructions therein, or follow instructions in:
/xGDBvm/0README-iPlant
For other users, in order to access this site over http, you may need to do the following (not required for iPlant instances):
1) start apache
2) start mysql
3) adjust firewall settings
In addition, you should update the xGDBvm code base from the github repository using 'sudo git pull origin master'
The github repository is at https://github.com/BrendelGroup/xGDBvm/ ( contributions welcome!)
Other directories required for xGDBvm to function include:
/home/xgdb-data/mysql/ (mysql databases)
/usr/local/bin/ and /usr/local/src/ where xGDBvm-related binary code is installed
See wiki (http://goblinx.soic.indiana.edu/wiki/doku.php) for additional details
Other links:
- xGDBvm github repository: https://github.com/BrendelGroup/xGDBvm/ (contributions welcome!)
- The Brendel Group at Indiana University: http://brendelgroup.org/
- Atmosphere virtual server environment: https://atmo.iplantcollaborative.org/
- Cyverse (formerly iPlant Collaborative): http://www.cyverse.org/