This document describes setting up SlideAtlas on linux, in particular on ubuntu releases 12.04 and 14.04, but it should be easy to interpret these instructions for platforms as well.
Python, pip and subversion-tools required, they can be installed by using
$ sudo apt-get install subversion-tools python2.7 python-pipSlideAtlas depends on several third party softwares and expects them to be installed on the system.
Required packages libtiff5-dev and openslide-tools are both available in ubuntu release 14.04
Install them using
$ sudo apt-get install openslide-tools libtiff5-devLatest versions of libtiff and openslide must be compiled from source. Following packages are required for successful compilation
$ sudo apt-get install autoconf automake libtool pkg-config libgtk2.0-dev
$ sudo apt-get install libxml2-dev libjpeg-dev liblzma-dev liblz-dev zlib1g-dev lzma libmatio-dev
$ sudo apt-get install libexif-dev libfftw3-dev swig python-dev liborc-0.4-dev libsqlite3-devwget ftp://ftp.remotesensing.org/pub/libtiff/tiff-4.0.3.tar.gz
tar xvzf tiff-4.0.3.tar.gz
cd tiff-4.0.3/
./configure
make
sudo make installgit clone git://github.com/openslide/openslide.git
cd openslide
autoreconf -i
./configure
make
sudo make installWarning
If any plugins are enabled, their dependencies should be installed accordingly. For more details see plugins
Once third party libraries are installed on the system, the required python packages mentioned in requirements.txt can be installed with
$ sudo pip install -r requirements.txtNote
none
Some more packages may be required at this stage
Detailed documentation can be built using sphinx
$ cd docs
$ make htmlCMake is required for testing.
$ cd testing
$ ctest -S ctest_driver.cmake$(export SLIDEATLAS_CONFIG_PATH=/home/dhan/projects/slideatlas-config-kitware/localhost/site_slideatlas.py ; gunicorn -k flask_sockets.worker run_websockets:app -b localhost:8080 --log-level=debug)Unless actively debugging, the fast way to run slide-atlas for serving tiles is to use gunicorn. This can start multiple workers.
$ EXPORT SLIDEATLAS_CONFIG_PATH=/path/to/site_config
$ gunicorn --reload run_gunicorn:app -b 0.0.0.0:8080 -w 4 --log-level=DEBUG$ EXPORT SLIDEATLAS_CONFIG_PATH=/path/to/site_config
$ python run.py$(export SLIDEATLAS_CONFIG_PATH=/home/dhan/projects/slideatlas-config-kitware/localhost/site_slideatlas.py ; python run.py)"/path/to/site_config" should be the absolute path to a configuration file with any locally-specific configuration changes.
If such a configuration file is not provided, SlideAtlas will use sensible defaults (e.g. connecting to a MongoDB at 'localhost:8080').
<VirtualHost admin.slide-atlas.org:80>
ServerName admin.slide-atlas.org
ServerAdmin dhanannjay.deo@kitware.com
WSGIDaemonProcess slideatlas user=www-data group=www-data threads=1
WSGIScriptAlias / /var/slideatlas-admin/run_apache.wsgi
<Directory /var/slideatlas-admin>
WSGIProcessGroup slideatlas
WSGIApplicationGroup %{GLOBAL}
Order deny,allow
Allow from all
</Directory>
ErrorLog ${APACHE_LOG_DIR}/error.log
# Possible values include: debug, info, notice, warn, error, crit,
# alert, emerg.
LogLevel warn
CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>