Arthropod Genomics 2011/Genome Project 101 Workshop

This page or section is under construction.

This page will be used for the Genome 101 Workshop at Arthropod Genomics 2011.

VMware Image

A VMware image will be made available to participants of the workshop. We will use this image during the workshop

System Configuration

This section attempts to track what we did to create the VMware image

Operating System	Ubuntu 11.04, 64 bit client. This is a popular Linux distribution
Memory	2 GB. If you run this on a system that has 2 gigabytes or less of memory, please decrease this number
Disk	80 GB. This is allocated 2 GB at a time, as needed, but VMware.
Networking	NAT
Username	gmod
Password

Installed Prerequisite Software

GMOD components have a variety of prerequisite software that needs to be installed. Here is a list of what was installed so we could install and run GMOD software.

Software	How	Comments
Mercurial	sudo apt-get install mercurial	Revision control system used by Galaxy
Microsoft TrueType core fonts	sudo apt-get install ttf-mscorefonts-installer	Used by Galaxy.
python-dev	sudo apt-get install python-dev	Used in Galaxy.
python-setuptools	sudo apt-get install python-setuptools	Used in Galaxy.
python-pip	sudo apt-get install python-pip	Used in Galaxy.
bx-python scripts	sudo pip install bx-python	Scripts used by Galaxy
Python 2.6	sudo apt-get install python2.6	Ubuntu 11.04 comes with Python 2.7, which Galaxy, does not like. This installs 2.6 in parallel.
	sudo apt-get install libgd2-xpm-dev libgd-gd2-perl libgd-tools libgd-svg-perl
	sudo apt-get install autoconf apache2
	sudo apt-get install postgresql postgresql-client
	sudo apt-get install libcgi-session-perl libdbd-pg-perl libdigest-md5-file-perl libclass-base-perl libmodule-build-perl libstatistics-descriptive-perl libtemplate-perl libxml-simple-perl liblog-log4perl-perl libparse-recdescent-perl libsql-translator-perl perl-doc

GMOD Components

Galaxy

The default python on Ubuntu 11.04 is 2.7. We need 2.6 to run Galaxy. Using the instructions from the GetGalaxy wiki page, Python 2.6 was downloaded and added at the front of the path.

mkdir ~/galaxy-python
ln -s /path/to/python2.5 ~/galaxy-python/python

~/.bashrc was edited and these lines were added to the end.

# Use Python 2.6 for Galaxy
export PATH=~/galaxy-python:$PATH

Galaxy was then downloaded:

cd ~/Documents
mkdir work
cd work
hg clone http://bitbucket.org/galaxy/galaxy-dist

And we then customized the landing image for this conference. (Details are not important.)

And now we can start it:

cd galaxy-dist
sh run.sh

And Galaxy is now installed and running. Goto http://localhost:8080.