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Basic Installation Instructions

Prerequisites

  1. PostgreSQL > 8.2
  2. Apache2 Webserver
  3. PHP 5

You can install these main dependencies with:

sudo apt-get install libapache2-mod-php5 php5-pgsql imagemagick

To use the Python-based helper scripts, you should also install the following packages:

sudo apt-get install python-psycopg2 python-yaml

Installation on Ubuntu 10.10

0. Clone the repository

The git repository is hosted at https://github.com/acardona/CATMAID - clone this repository somewhere outside your web root, e.g. in /home/alice, so that the source code is in /home/alice/catmaid:

    git clone git://github.com/acardona/CATMAID.git

1. Install and configure PostgresSQL

You may find the advice here useful. In short, you should do the following:

    sudo apt-get install postgresql pgadmin3 phppgadmin postgresql-contrib

phppgadmin is optional, but is suggested if you are not comfortable with interacting with PostgreSQL from a terminal. Update the password for your catmaid user in /home/alice/catmaid/docs/createuser.sql. If you want the database to be called something other than catmaid you also change that in the lines beginning CREATE DATABASE and \c in the same file.

Then you should run the commands in that file as the postgres user:

sudo -u postgres psql < docs/createuser.sql

(On some systems you may get the the error ERROR: language "plpgsql" already exists which can be safely ignored.)

Check if you can login - the database should still be empty, however:

http://localhost/phppgadmin/

Make sure that the catmaid database is accessible using MD5 hashed passwords - you have to add this line as the first rule in /etc/postgresql/8.4/main/pg_hba.conf:

local catmaid catmaid_user md5

(If you have changed the database name or user, you should change them in that rule as well.)

After the above please restart the database:

sudo /etc/init.d/postgresql-8.4 restart

Update the catmaid database configuration in: inc/setup.inc.php.template and rename the file to inc/setup.inc.php

2. Configure Apache

There are two possibilities here - setting up CATMAID on its own virtual host, or setting it up as a subdirectory of an existing host:

2.1 Named Virtual Hosts approach:

(The advice here may be of use.)

Your clone of the CATMAID source code should be outside any web-accessible directory. For example, let's say that you have the source code in /home/alice/catmaid/

Create a directory for the log files, for example with:

sudo mkdir -p /var/log/apache2/catmaid/

Create in /etc/apache2/sites-available a file called "catmaid":

 <VirtualHost *:80>
     ServerName catmaid

     DocumentRoot "/home/alice/catmaid/httpdocs/"

     php_admin_value register_globals off
     php_admin_value include_path ".:/home/alice/catmaid/inc"
     php_admin_value session.use_only_cookies 1
     php_admin_value error_reporting 2047
     php_admin_value display_errors true

     <Directory /home/alice/catmaid/httpdocs/>

         Options FollowSymLinks
         AllowOverride AuthConfig Limit FileInfo

         Order allow,deny
         allow from all

     </Directory>

     CustomLog /var/log/apache2/catmaid/access_log combined
     ErrorLog /var/log/apache2/catmaid/error.log

 </VirtualHost>

Then make apache aware of the virtual host:

 sudo a2ensite catmaid

... then restart apache:

 /etc/init.d/apache2 restart

... and finally add this entry to "/etc/hosts" :

 127.0.0.1    catmaid

2.2 As a directory of an existing virtual host

 <VirtualHost *:80>
         ServerAdmin webmaster@localhost

         DocumentRoot /var/www
         <Directory />
                 Options FollowSymLinks
                 AllowOverride None
         </Directory>
         ...
         ...

         # Add CATMAID configuration here:

         Alias /catmaid/ /home/mark/catmaid-local-instance/httpdocs/
         <Directory /home/mark/catmaid-local-instance/httpdocs/>

                 php_admin_value register_globals off
                 php_admin_value include_path ".:/home/mark/catmaid-local-instance/inc"
                 php_admin_value session.use_only_cookies 1
                 php_admin_value error_reporting 2047
                 php_admin_value display_errors true

                 Options FollowSymLinks
                 AllowOverride AuthConfig Limit FileInfo
                 Order allow,deny
                 Allow from all
         </Directory>

         ...
         ...
 </VirtualHost>

You should then restart Apache:

 /etc/init.d/apache2 restart

3. Now try it out!

Try to start CATMAID::

 firefox http://catmaid/

... or with:

 firefox http://localhost/catmaid/

... depending on the approach you took above. You will get an error to tell you that no projects are found. If you want to create some example projects and stacks for testing, you should run:

 scripts/insert-example-projects.py

To create a login, you should use the scripts/create-user.py script, such as with:

 scripts/create-user.py humpy "Sir Humphrey Appleby"

This will prompt you for a password for this new user.

4. Adding a new project

You can generate the image tiles for a stack with the scripts/tile_stack script or by exporting from TrakEM2 with its "Export > Flat Images" option and selecting the "Export for web" checkbox.

Then you can create a new project with the script scripts/create_project_stack.py

  Usage: create-project.py <host> <database-name>

The script enables the generation of a new project or uses an existing project. For a new project, it creates the classes and relations necessary for SVG-based annotation and associates the project with the users. It enables the creation of new stacks associated with the project.

More details about the data model can be found in docs/data-model.lyx - a PDF generated from that file can be found here: