This page was last updated on Wednesday, 22-Jan-2014 16:11:26 CST

Installation notes for SyMAP version 4.0

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Prerequisites

• • $ sudo apt-get install libfreetype6-dev
  • $ sudo apt-get install libpng12-dev
  • $ sudo cpan Imager Imager::Font::FT2 Imager::File::PNG
• $ sudo cpan Math::Bezier
• $ sudo cpan GD::Text::Align
• Others documented as dependencies that were already installed
  DBI Cwd Data::Page Storable File::Temp CGI CGI::Carp GD

Installation

1. Requires registration. Downloaded to /programinstallers/ manually from http://www.agcol.arizona.edu/software/symap/v4.0/download/
2. $ cd /usr/local/bin
3. $ tar -zxvf /programinstallers/symap_40.tar.gz
4. Optional, remove files for other operating systems
   

   rm symap_40/ext/mummer/mac -rf
   rm symap_40/ext/muscle/mac -rf
   rm symap_40/ext/blat/mac -rf
   rm symap_40/ext/test/testbinmac -rf
   rm symap_40/java/lib/osx -rf
   rm symap_40/ext/mummer/lintel -rf
   rm symap_40/ext/muscle/lintel -rf
   rm symap_40/ext/blat/lintel -rf
   rm symap_40/ext/test/testbin32 -rf
   rm symap_40/java/lib/i386 -rf
   rm symap_40/symap*bat

5. Create a launcher
   $ sudo nano /usr/share/applications/Bioinformatics/SyMAP.desktop
   This creates a new file. Add this:
   #!/usr/bin/env xdg-open
    
   [Desktop Entry]
   Version=1.0
   Type=Application
   Terminal=true
   Exec=/usr/local/bin/symap_40/symap
   Path=/usr/local/bin/symap_40
   Name=SyMAP 4.0
   Comment=Synteny Mapping and Analysis Program
   Icon=/
   Categories=Bioinformatics
6. Edit SyMAP configuration file
   $ nano /usr/local/bin/symap_40/symap.config
   ...

   db_name             = SyMAP40
   db_server           = vcru.wisc.edu
   db_adminuser        = ○○○○
   db_adminpasswd      = ●●●●
   db_clientuser       = ▲▲▲▲
   db_clientpasswd     = ▼▼▼▼
   
   # Locations for symap html and cgi scripts on disk.
   # Files will be copied to these directories.
   html_path	= /var/www/html/symap          # e.g., /www/htdocs/symap
   cgi_path        = /var/www/cgi-symap           # e.g., /www/cgi-bin/symap
   
   # URLs for symap html homepage and cgi-bin
   html_url        = http://vcru.wisc.edu/symap             # e.g., http://www.myserver.myschool.edu/symap
   cgi_url         = http://vcru.wisc.edu/cgi-symap         # e.g., http://www.myserver.myschool.edu/cgi-bin/symap

   ...
7. Setup MySQL on web server
   mysql> CREATE USER '○○○○'@'carrot' IDENTIFIED BY '●●●●';
   
8. mysql> GRANT ALL on SyMAP40.* to '○○○○'@'carrot';
9. mysql> CREATE USER '▲▲▲▲'@'vcru.wisc.edu' IDENTIFIED BY '▼▼▼▼';
10. mysql> GRANT SELECT on SyMAP40.* to '▲▲▲▲'@'vcru.wisc.edu';
11. mysql> FLUSH PRIVILEGES;
12. Install web files on web server
    $ sudo mkdir /var/www/cgi-symap
13. $ mkdir /var/www/html/symap
14. Password protect them
    $ sudo nano /etc/apache2/sites-available/default
    Add password protection configuration for Apache

            ScriptAlias /cgi-symap/ /var/www/cgi-symap/

    ...

            <Directory "/var/www/cgi-symap">
                    Options +ExecCGI -MultiViews
                    AllowOverride AuthConfig
                    AuthType Basic
                    AuthName "♠♠♠♠"
                    AuthUserFile /var/www/.htpasswd
                    Require user ♣♣♣♣
            </Directory>
            <Directory "/var/www/html/symap">
                    Options +ExecCGI -MultiViews
                    AllowOverride AuthConfig
                    AuthType Basic
                    AuthName "♠♠♠♠"
                    AuthUserFile /var/www/.htpasswd
                    Require user ♣♣♣♣
            </Directory>

15. $ sudo perl /usr/local/bin/symap_40/scripts/install.pl
16. $