wiki:InstallationInstructions05

Bisque Installation


Guided Complete Install

Required System Packages

Following packages should be pre-installed on your system for the installation to be function correctly:

Package Generic Debian Redhat MacOS Windows 64 bit
Install command - apt-get install yum install N/A N/A
python2.7-dev http://www.python.org/download/ python-dev python XCode ActivePython
setuptools http://pypi.python.org/pypi/setuptools/ ships with ActivePython
virtualenv http://pypi.python.org/pypi/virtualenv python-virtualenv easy_install virtualenv

Required python packages that depend on c/c++ libraries and may fail with pip or easy_install. Under windows they are installed from suggested library. Under Linux pip or easy_install after installing suggested c/c++ package:

Package Debian Redhat MacOS Windows 64 bit
lxml libxml2-dev,libxslt1-dev libxml2-devel,libxslt-devel easy_install installer: lxml
numpy easy_install easy_install easy_install installer: numpy
pytables libhdf5-dev ? easy_install installer: tables

Optional System packages

The following packages are not required, but do add capabilities or performance to the base system.

We list the possibilities here:

Package Reason Generic Debian Redhat MacOS Windows
Install command apt-get install yum install N/A N/A
gcc mlabwrap, sqlite,etc
g95 scipy http://www.g95.org/ gfortran gortran
matlab analysis modules http://www.mathworks.com/ N/A N/A N/A N/A
postgres http://www.postgresql.org/download/ postgres-9.1, libpq-dev
mysql http://www.mysql.com/ mysql-server|libmysqlclient-dev
apache http://httpd.apache.org/ apache2 apache2
nginx proxy, uploader http://nginx.org/ nginx nginx
libopenslide large images openslide.org libopenslide-dev (biodev), libopenjpeg-dev(jessie)
libtiff4 required for feature service http://www.remotesensing.org/libtiff/ libtiff4-dev

Prepare a Python Virtual Environment

  1. Create a bisque directory and download this Bootstrap script
    mkdir bisque; cd bisque
    wget http://biodev.ece.ucsb.edu/projects/bisquik/export/tip/bisque-stable/contrib/bootstrap/bisque-bootstrap.py
    
  2. Bootstrap bisque by running the boostrap script (python2.6 or python2.7 REQUIRED), and download the initial files.
    bisque$ python bisque-bootstrap.py [--python=python2.6] [bqenv]
    
    This will create a python virtual environment and install all python dependencies for bisque. If this fails, (due to missing headers of packages), you can restart by activating the env (see below) and running pip install -r requirements.txt
  3. Activate the virtualenv before the next steps and before you executate any bisque commands or scripts
    • Linux or MacOS X
      bisque$ source bqenv/bin/activate
      
    • Windows
      bisque > bqenv\Scripts\activate.bat
      
    You must activate the environment if you logout or create a new shell before using command line tools with bisque.

You are about to configure the system. Please take a look at the dependency table to insure you have the necessary system packages installed. If you upgrading from a previous Bisque installation, please review the instructions at Installation/BisqueUpgrade before proceeding.

  1. (optional) Install module dependencies. This will allow the module to setup and tested in the next step. You can skip this step and install the dependencies at a later time, by re-running $bisque-setup --modules See Add on Modules
  2. Configure the bisque system. You will be asked a series of question about your intended installation. If unsure at any question, you can type '?' to receive help. Otherwise please check the BisqueFaq?
    (bqenv)$ # Activate YOUR Virtual Environment if you have not done so.. no command will work unless you do so.
    (bqenv)$ paver setup [engine|server]
    (bqenv)$ bq-admin setup [engine]
    
    If something fails during setup.. Don't panic. You can run the different aspects of the setup again. The list of setup modules is mercurial, binaries, site, database, modules, bioformats i.e Simply run bq-admin setup database
  3. Production deployment
    bq-admin deploy public
    

This is required in the production environment in order to compress and make UI javascript available.

  1. On server installs Install imgcnv image service program and other image converters. imagecnv must be installed before proceeding.
    1. If a precompiled version is available from us, bq-admin setup will have installed imgcnv.
    2. If your are a debian-like system, please check CbiDebian to use our package repository
    3. If a pre-built package is not available you can compile imgcnv from source. You will need download the the source code, have qmake and c/c++ compiler available.
      (bqenv)$ hg clone http://biodev.ece.ucsb.edu/hg/imgcnv
      (bqenv)$ cd imgcnv
      (bqenv)$ sh ./build-imgcnv-SYS.sh
      (bqenv)$ cp imgcnv ../bqenv/bin
      (bqenv)$ cd ..
      
  2. Start the system
    (bqenv)$ bq-admin server start
    
  3. Acess the system with your browser (firefox, safari, chrome, etc). The default intall only allow access from localhost (http://localhost:8080)
  4. Congratulations! You have installed bisque. If you are using a sqlite database then the system is suitable for small sites of several thousand images and only 1 or 2 users. For larger systems please refer to Installation/AdvancedInstalls
  5. Please take a look at Configuring a Bisque Site.
  6. Shutdown the servers with:
    (bqenv)$ bq-admin servers stop
    

Restarting with supervisor (VM install)

Current VM uses supervisor to start and stop bisque instances. This is useful because supervisor starts bisque automatically upon machine startup. In order to restart bisque servers running with supervisor use the following command:

supervisorctl restart bisque:

You can also restart a specific bisque service, for example to only restart the engine service use:

supervisorctl restart bisque:e1_uwsgi

Add-on Module Dependencies

Some of the add analysis modules also have there own requirements Please ensure your virtualenv is active before installing these:

You will need to rerun bisque-setup.py. You can answer N to all questions except the setup modules

(bqenv)$ bq-admin setup modules

Advanced Configuration Topics

VirtualBox

VirtualBox is a great way to get a completely configure bisque instance running in a few minutes.

  1. Bisque virtualBox installation and setup.

Previous Versions

System Specific Install

These are a collection of notes and sometimes full instructions for installing Bisque on various platforms. If in doubt refer to the full instructions

Some of these can be out of date. Please review against the instructions found on this page.

Our previous installation are in OldBisqueInstall?

Last modified 3 years ago Last modified on Feb 25, 2015 9:33:51 AM