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Difference between revisions of "Arthropod Genomics 2011/Genome Project 101 Workshop"
m (→Installed Prerequisite Software) |
m (→Galaxy) |
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Line 71: | Line 71: | ||
=== [[Galaxy]] === | === [[Galaxy]] === | ||
+ | |||
+ | The default python on Ubuntu 11.04 is 2.7. We need 2.6 to run Galaxy. Using the instructions from the [https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy GetGalaxy wiki page], Python 2.6 was downloaded and added at the front of the path. | ||
+ | <pre class="enter"> | ||
+ | mkdir ~/galaxy-python | ||
+ | ln -s /path/to/python2.5 ~/galaxy-python/python | ||
+ | </pre> | ||
+ | <tt>~/.bashrc</tt> was edited and these lines were added to the end. | ||
+ | <pre class="enter"> | ||
+ | # Use Python 2.6 for Galaxy | ||
+ | export PATH=~/galaxy-python:$PATH | ||
+ | </pre> | ||
+ | |||
+ | Galaxy was then downloaded: | ||
<pre class="enter"> | <pre class="enter"> | ||
cd ~/Documents | cd ~/Documents | ||
Line 77: | Line 90: | ||
cd work | cd work | ||
hg clone http://bitbucket.org/galaxy/galaxy-dist | hg clone http://bitbucket.org/galaxy/galaxy-dist | ||
+ | </pre> | ||
+ | |||
+ | And now we can start it: | ||
+ | <pre class="enter"> | ||
cd galaxy-dist | cd galaxy-dist | ||
sh run.sh | sh run.sh |
Revision as of 09:14, 3 June 2011
This page or section is under construction.
This page will be used for the Genome 101 Workshop at Arthropod Genomics 2011.
Contents
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. |
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 now we can start it:
cd galaxy-dist sh run.sh
And Galaxy is now installed and running. Goto http://localhost:8080. To kill it, type
<ctrl-c>
Running run.sh will start it up again.