GenoREAD Files

README for GenoREAD Alpha Version

GenoREAD depends on the Apache webserver, PHP5, and Perl 5.
  
In addition, the following software packages must also be installed; not all of them are OpenSource, although those that are not are available to academic organizations under a free academic license.
o phred and cross_match (cross_match is distributed with phrap): http://www.phrap.org/consed/consed.html#howToGet

o MIRA (Open Source): http://sourceforge.net/projects/mira-assembler/

o GD Graphics Library (Open Source): http://libgd.bitbucket.org/

To install the GenoREAD framework software:
o Copy downloaded files and folder structure to the webroot of the website directory

o Edit parameters.php to set your local php variables, such as directory paths, website names, and email addresses.

o Edit perl_scripts/process_one_clone.php to set the local environment variables for the PHRED_PARAMETER_FILE (phredpar.dat) and the PATH (to include the locations of phred/bin, phrap/bin, and MIRA/bin.)

o Make sure that web users have permissions to upload files into your uploads, results, and projects directories.

o You may want to edit the header.htm and the footer.htm to customize it for your organization.