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THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHORS OR CORRESPONDING INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

 

Installation of Another Portal for EST Data (APED)

Example system is running CentOS 4.5 using apache and with SELinux disabled.

  1. create pipeline user account
    1. main account cron jobs will be run from

                                                                   i.      check for new data, phred, lucy etc…

    1. APED installation as this user
  2. secure the pipeline account
    1. beyond the scope of this document
    2. suggestion is to disable direct logins to the pipeline account and require access via su – pipeline
    3. if you don’t understand the security ramifications you are strongly recommended to read up on *nix security
  3. ensure pipeline account is in the apache group (or whatever the httpd GID is)
    1. both pipeline and apache will need to be able to read/write files on disk
  4. Checkout the code from the cvs

 

cvs -d:pserver:anonymous@aped.cvs.sourceforge.net:/cvsroot/aped login

cvs -z3 -d:pserver:anonymous@aped.cvs.sourceforge.net:/cvsroot/aped co -P aped

 

  1. Configure APED environment variable to be the root of the CVS checkout
    1. Recommendation: add this to /home/pipeline/.bashrc

 

export APED=/home/pipeline/aped

 

  1. Configure HTTPD
    1. See $APED/doc/README.httpd.conf
    2. You will need to configure symlinks from the cgi-bin and html directories to point into $APED/cgi-bin and $APED/html

 

ln -s $APED/cgi-bin /var/www/cgi-bin/aped

ln -s $APED/aped/html /var/www/html/aped

 

    1. If you are using symlinks then you will need to ensure that following symlinks is enabled for your webserver
    2. Edit and add the $APED/doc/aped.conf to your apache conf dir (probably /etc/httpd/conf.d/)
    3. Restart apache

service httpd restart

  1. Configure Mysql
    1. Create a database e.g. aped
    2. Load the schema from $APED/doc/schema.sql
    3. Configure the mysql permissions for the 2 user accounts (pipeline and apache)

                                                               i.      Follow the instructions in $APED/mysql_install/README

  1. Install bioperl
    1. See www.bioperl.org
  2. Install a Bio::Assembly::IO::tgicl module
    1. Copy $APED/patching_ace.pm/tgicl.pm into the correct path of the perl installation

                                                               i.      Similar to /usr/lib/perl5/site_perl/5.8.5/Bio/Assembly/IO/tgicl.pm

  1. Ensure that you have all of the necessary perl modules installed
    1. Recommendation is to install via MCPAN as root
    2. Required

                                                               i.      BioPerl

1.      if you over-write the BioPerl installation ensure that you still have the Bio::Assembly::IO::tgicl module

                                                             ii.      GD

                                                            iii.      GD::Graph

                                                            iii.      Mail::Mailer

  1. Configure crontab for pipeline
    1. Edit and add $APED/doc/sample_crontab to pipeline’s crontab
  2. Things should be ready to run

Additional pointers

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