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Installation
This page contains user and developer installation instructions for brat.
Since brat (and this page) is very much under development the information on this page may not be up to date. If not, bash the developers ASAP.
This is where we should have written instructions for previous releases.
Check out brat using git.
git clone -n [email protected]:TsujiiLaboratory/brat.git
If you are behind an exceptionally nasty firewall (be warned though, this is a lot slower), try:
git clone -n https://${GIT_USERNAME}@github.com/TsujiiLaboratory/brat.git
When pulling over HTTPS you may get a GTK error like below:
(gnome-ssh-askpass:4711): Gtk-WARNING **: cannot open display:
This is due to SSH_ASKPASS being set to use gnome-ssh-askpass, see the discussion here. Just unset SSH_ASKPASS or set it to an empty string and you will be prompted for your password without the need for a GUI. Another fun note, on HTTPS you will receive a SSL certificate and old machines won't carry all the modern ones. To disable this prefix your git command with env GIT_SSL_NO_VERIFY=true, which of course isn't safe but works. For more
SSH issues, see here.
Enter the brat directory, and check out the master branch:
cd brat
git checkout -b master origin/master
When running brat it needs to write data to several directories, let's create them.
mkdir data work
We now need to set the permissions of these directories so that they can be read and written by Apache. The command-line below is likely to give you the Apache 2 group if you have Apache currently running. If not, see the "Finding Your Apache 2 Group" section of this page:
groups `ps aux | grep apache | grep -v 'grep' \
| cut -d ' ' -f 1 | grep -v 'root' | head -n 1` \
| cut -d : -f 2 | sed 's|\ ||g'
Then simply change the group of the directories (change ${YOUR_APACHE_GROUP}
into the output you got above) and set the correct permissions:
sudo chgrp -R ${YOUR_APACHE_GROUP} data work
chmod -R g+rwx data work
If you can't succeed with the above or you are not concerned with security (say that it is a single-user system), you can run the command below instead or refer to your operating system manual and look-up Apache 2 for their instructions on how to get the Apache group. This will make the directories write-able and read-able by every user on your system:
chmod 777 data work
Extract all the library dependencies.
( cd server/lib && tar xfz simplejson-2.1.5.tar.gz )
And extract and compile GeniaSS:
( cd external && tar xfz geniass-1.00.tar.gz && cd geniass && make )
Put a configuration in place.
cp config_template.py config.py
Edit the configuration to suit your environment.
vim config.py
Your installation should now be ready, just place your data in the data
directory and make sure it has the right permissions using chmod as you did
above. If your data consists of no prior annotations and only .txt files,
create the annotation files (.ann) as below.
( find data -name '*.txt' | sed -e 's|\.txt||g' \
| xargs -I {} touch '{}.ann' )
This part largely focuses on Ubuntu, but use your *NIX-foo to turn it into what you need if you don't have the misfortune to have the "Brown Lunix Distribution".
Hopefully you are lucky enough a sensible OS and can get it through a package manager:
sudo apt-get install git
Install apache2, maybe you have a package manager.
sudo apt-get install apache2
Let's edit the httpd.conf.
sudo vim /etc/apache2/httpd.conf
If you are installing brat into your home directory, add the following four lines.
<Directory /home/*/public_html>
AllowOverride Options Indexes
AddHandler cgi-script .cgi
AddType application/xhtml+xml .xhtml
AddType font/ttf .ttf
</Directory>
And make sure that you have the userdir module enabled.
sudo a2enmod userdir
Finally tell apache2 to load your new config.
sudo /etc/init.d/apache2 reload
Ideally you should set all permissions as needed for the Apache 2 group, but finding it can be painful.
Find out what the Apache group name is, it is usually apache or www-data;
it can be found in apache2.conf or httpd.conf under /etc/apache2/ or
/etc/httpd/. Let's assume it's www-data. Then:
sudo chgrp -R www-data data work
chmod -R g+rwx data work
Actually, due to the joy of Linux segmentation you can find the group elsewhere as well. Here is a small heuristic that works on at least two distributions:
locate --regex '(apache2|httpd)\.conf$' | xargs cat | grep 'Group'
If what you get from this looks funky, say with a leading $, try this:
locate envvars | grep -E '(apache2|httpd)' | grep '/etc/' \
| xargs cat | grep -i 'group'
If this doesn't work either dive into /etc/group and hope that you can find
something that at least looks like apache or www-data:
cat /etc/group | cut -d : -f 1 | sort
On a Mac, Apache configuration is quite different, and Aptitude is not available.
A binary package is available from here. Alternately, you can get it through a package manager: Homebrew or MacPorts. You will need XCode (from your Mac OS X disk, or from Apple. Then you can use one of these commands to install Git:
brew install git
or
port install git
Clone this repository into ~/Sites. Edit
/private/etc/apache2/users/$USER.conf. Then invoke sudo apachectl reload.
The default user and group name for Apache is _www (as found in
/private/etc/apache2/httpd.conf), for use in chgrp.
brat has a very flaky back-up system (actually my fault for my early morning
hack), there is an alternate script that you can use with good old cron.
Do as follows.
Add a line like the one below to the crontab for your Apache user:
0 5 * * * ${PATH_TO_BRAT_INSTALLATION}/tools/backup.py
You will now have a back-up made into your work directory every morning at five o'clock.
To support export to formats other than SVG from the UI, a tool capable of the relevant conversion must be set up on the server. This functionality has primarily been tested with inkscape.
The following command has been found to produce a reasonable SVG-to-PNG conversion:
'inkscape --export-area-drawing --without-gui --file=%s --export-png=%s'
(where the first %s is filled in with the input and the second with the output filename.)
NOTE about inkscape setup: at least version 0.46 will crash with an obscure error message unless the directory .gnome2/ exists in the apache home directory.