HTTPS SSH
GALAXY
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http://galaxyproject.org/
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http://bitbucket/jelle/galaxy-central-tron-lims/


= Introduction = 

Galaxy offers by default a Sample Tracking system. In the NGS LIMS project we decided to use and extend this system. 

== Quick start ==

This is a summary to get a populated version of the Galaxy LIMS

* Check the dependencies (see below)
* hg clone https://bitbucket.org/jelle/galaxy-central-tron-lims galaxy-central-tron-lims
* cd galaxy-central-tron-lims/ && ./run.sh --daemon && tail -f paster.log
* Check correct running interface on http://localhost:8080 and inspect the paster.log file
* python scripts/lims/add_defaults.py universe_wsgi.ini demo
* Login using you@company.none/demolims
* Test watchflowcell script: 
** cd scripts/api && python watchscript_flowcell.py

== Dependencies ==
===Recommend===
We highly recommend you use virtualenv or virtualenvwrapper to prevent python package conflicts.
sudo pip install virtualenvwrapper
mkdir ~/python-envs
export WORKON_HOME=~/python-envs
source /usr/local/bin/virtualenvwrapper.sh
mkvirtualenv galaxy-lims
pip install -r requirements.txt
#do check if PIL installs with zlib support

===Details===
The following python modules are required.
* pyyaml
* pillow *with zlib(PNG/ZIP) support*
* xhtml2pdf
* qrcode
* xlrd

In addition you may also want to use virtualenv as also proposed by the Galaxy 'Production Server' http://wiki.galaxyproject.org/Admin/Config/Performance/Production%20Server#Use_a_clean_environment

One way to install the above mentioned modules is by using easy_install. In order for easy_install to build these modules you might also need the *python-dev* package (e.g. apt-get install python-dev).

To get easy_install:

When running python 2.6:
wget 'http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.egg#md5=bfa92100bd772d5a213eedd356d64086'
sh setuptools-0.6c11-py2.6.egg

or for python 2.7:
wget 'https://pypi.python.org/packages/2.7/s/setuptools/setuptools-0.6c11-py2.7.egg#md5=fe1f997bc722265116870bc7919059ea'
sh setuptools-0.6c11-py2.7.egg

And then:

easy_install pyyaml
easy_install pillow #check for zlib *-see note below*
easy_install xhtml2pdf
easy_install qrcode
easy_install xlrd

Make sure PIL builds with zlib support. You might need to check that libz.so is located in /usr/lib see also: [[http://www.foxhop.net/ubuntu-python-easy_install-pil-does-not-install-zlib-support|easy_install PIL does not install zlib]] 

    *If PIL fails to install with zlib support, you will first have to remove the package! *
    Removing python packages can be made easy with pip e.g. easy_install pip && pip uninstall PIL

====
You may wish to make changes from the default configuration.  This can be done
in the universe_wsgi.ini file.  Tools are configured in tool_conf.xml.  Details
on adding tools can be found on the Galaxy website (linked above).

Not all dependencies are included for the tools provided in the sample
tool_conf.xml.  A full list of external dependencies is available at:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies