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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.
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. |
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 | ||
cpan> install GD | ||
cpan> install Bio::Perl Bio::Graphics JSON | ||
cpan> install Bio::DB::Das::Chado | ||
cpan> install GO::Parser Module::Load DBIx::DBSchema XML::Parser::PerlSAX |
PostgreSQL Configuration
The postgresql server will be set up with fairly unrestricted access to make life easier during the tutorial. If used "in real life", the configuration should be tightened down quite a bit.
Edit config file
sudo su - vi /etc/postgresql/8.4/main/pg_hba.conf
Change the bottom lines to look like this:
# "local" is for Unix domain socket connections only local all all trust # IPv4 local connections: host all all 127.0.0.1/32 trust # IPv6 local connections: host all all ::1/128 trust
by replacing the text in the last column to "trust" as it is here (that's the insecure part!). Then restart the postgresql server:
/etc/init.d/postgresql-8.4 restart
Then, switch users to the "postgres" user and create a new user called "gmod":
su - postgres createuser gmod Shall the new role be a superuser? (y/n) y exit # to leave postgres user shell exit # to leave root shell
Install DBIx::DBStag
This is a perl module that can only be installed after PostgreSQL is configured, so it is installed now. First, create a database called "test":
createdb test
Then install via the cpan shell:
cpan cpan> install DBIx::DBStag
Note that installing via the cpan shell is difficult if you typically use cpan as root, like "sudo cpan". If instead you use cpan as a regular user but have it configured to do "sudo make install" and "sudo ./Build install" it is easy and works correctly.
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.
Chado
Get Chado from SourceForge; point a browser at
http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/chado-1.11.tar.gz/download
and extract the files:
cd ~/Downloads tar zxvf chado-1.11.tar.gz cd chado-1.11
Set up some environment variables:
vi ~/.bashrc
and add these lines to the bottom:
export GMOD_ROOT=/usr/local/gmod export CHADO_DB_NAME=chado export CHADO_DB_USERNAME=gmod
save .bashrc and source it so that the values are available in the shell:
source ~/.bashrc
Now to install Chado:
perl Makefile.PL
Accept all of the defaults except for the "default organism" question. Put "pythium" here.
make sudo make install make load_schema #ignore the error about a chado database not existing make prepdb make ontologies answer with 1,2,4
Add our organism to the database:
psql chado psql> INSERT INTO organism ( abbreviation, genus, species, common_name) VALUES ('P.ultimum','Pythium','ultimum','pythium');
Make a database dump that saves progress to this point:
pg_dump chado | bzip2 -c > ontologies_only_dbdump.bz2
GBrowse
GBrowse can be installed directly from the cpan shell like several of the GBrowse prerequisites were installed:
cpan cpan> install Bio::Graphics::Browser2
Accept all of the defaults when asked questions.
JBrowse
wget http://jbrowse.org/releases/jbrowse-1.2.1.zip