technotes.txt

MySQL is required
By default, serverlog file in installation root directory records all warnings and errors.
When setting up the server, the /output URL must be mapped to the location of output folder in the filesystem, or simply just use 'output' as the output folder name. Same case for example, cgi-bin.
after everything is set, run 'cgi-bin/submission.cgi' and copy all files out of html, then you will get the index.html
chmod 733 output
chmod 733 log/error.log
SQLite3 must be installed and put in system PATH because LocusZoom utilizes this database engine.
CGI DBI DBD::mysql IPC::System::Simple Email::Sender::Simple Email::MIME perl modules are required. Don't forget to tell all CGIs where libs are located by changing PERL5LIB variable
to force all queued and running jobs quit, just put '1' in jobClean() subroutine and submit a dummy job, all jobs will quit before this dummy job runs
make sure to have functional locuszoom and table_annovar.pl before setting up the server
read and modify enlight_server.conf and m2zfast.conf wherever necessary
add data tracks to both locuszoom database and annovar database folder
python 2.7, annovar, various perl modules are required. Please make sure they appear in apache's PATH. Or you can modify the first line of the script, or add $ENV{PATH}="path:".$ENV{PATH} in perl code
make sure annotate_variation.pl at the beginning of your PATH
make the installation folder as the document root for apache (or its virtual host)
install ucsc liftOver program, download chain file (modify annodb_admin accordingly)
download hg19 and hg18 builds of refgene, 1000g2012apr databases for ANNOVAR
modify enlight/conf/m2zfast.conf to make sure plink and newfugue paths are correct
change perl5lib path in cgi-bin/process.cgi to make sure the local modules can be found 

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commands for setting up Enlight
wget http://www.cpan.org/src/5.0/perl-5.22.0.tar.gz
tar -xzf perl-5.22.0.tar.gz
cd perl-5.22.0
./Configure -des -Dprefix=$HOME/localperl
make
make test
make install
cd ..
~/localperl/bin/cpan CGI DBI DBD::mysql IPC::System::Simple Email::Sender::Simple Email::MIME Email::Sender::Transport::SMTP::TLS DBD::mysql Array::Transpose
wget https://www.python.org/ftp/python/2.7.10/Python-2.7.10.tgz
gunzip Python-2.7.10.tgz 
tar xvf Python-2.7.10.tar 
cd Python-2.7.10
./configure --prefix=$HOME/localpython
make && make install
chmod 733 enlight/output
chmod 733 enlight/log/error.log


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for MySQL
mysql -u yunfeiguo -p
use yunfeiguo_enlight #or any other database name