Installing Morphbank

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BioDivImage software (MorphBank) SourceForge home page (we are working with the PHP version of Morphbank as developed in Florida, rather than the Drupal version being developed in Australia. Note that there is also an empty placeholder project put up on sourceforge by Katja that doesn't have code in it.)

Downloading

Subversion repository:

svn export https://biodivimage.svn.sourceforge.net/svnroot/biodivimage/trunk biodivimage

Installing

Wiki instructions for installation

The wiki instructions were easy to follow. Here are a few notes:

1. Use svn export rather than svn co.

2. To see what PEAR packages you have installed (provided you already have pear installed):

> pear list

and to install a PEAR:

> sudo pear install Foo

3. I used the following MySQL configs, a slight departure from the instructions:

old_passwords = 1
collation_server = utf8_general_ci
character_set_server = utf8
init_connect = 'SET NAMES utf8'

See also the comments concerning PHP on this MySQL documentation page.

4. I added two names to my /etc/hosts file, morphbank-t for the "app server," and mb-images-t for the "image server:"

127.0.0.1       morphbank-t
127.0.0.1       mb-images-t

Thus I am using the following configs for Apache (in Ubuntu).

/etc/apache2/httpd.conf: add the directive NameVirtualHost 127.0.0.1:80

/etc/apache2/sites-available/default: replace *:80 with 127.0.0.1:80 e.g.: <VirtualHost 127.0.0.1:80>

/etc/apache2/sites-available/morphbank-t: again use <VirtualHost 127.0.0.1:80>, and include

ServerName morphbank-t
DocumentRoot /var/www/mb32/www

<Directory /var/www/mb32/www/>
    AllowOverride All
 </Directory>

/etc/apache2/sites-available/mb-images-t: again use <VirtualHost 127.0.0.1:80>, and include

ServerName mb-images-t
DocumentRoot /var/www/mb32/ImageServer

<Directory /var/www/mb32/ImageServer>
    AllowOverride All
 </Directory>

If you are getting blank pages when you access your "site" http://morphbank-t/, make sure that AllowOverrides is properly set. Try accessing http://morphbank-t/test.php to see what value you have for include_path. I have:

.:/usr/share/php:/usr/share/pear
:/var/www/mb32/www
:/var/www/mb32/security
:/var/www/mb32/configuration
:/var/www/mb32/www/includes
:/var/www/mb32/www/data
:/var/www/mb32/library
:/var/www/mb32/adminProcesses

5. Loading the sample data takes a little while, at least a few minutes.

6. I edited sample.config.ini rather than use install.php, it was a little easier to guess what values to use. Here are values that depend on your Apache config (as set up above):

;########## Image Server ##########
imgServer = "mb-images-t"
imgServerUrl = "http://mb-images-t/"

;########## Application Server ##########
appServer = "morphbank-t"
appServerBaseUrl = "http://morphbank-t/"

;########## Application Settings ##########
domain = "/"

7. If the main page shows up fine, but accessing images times out, there is probably something wrong with the Apache configuration or the config.ini entries for the image server. Also make sure you've copied the htaccess file to the ImageServer directory.