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Difference between revisions of "Arthropod Genomics 2011/Genome Project 101 Workshop"

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(→‎Installed Prerequisite Software)
(→‎Installed Prerequisite Software)
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===PostgreSQL Configuration===
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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.
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====Edit config file====
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  sudo su -
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  vi /etc/postgresql/8.4/main/pg_hba.conf
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Change the bottom lines to look like this:
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  # "local" is for Unix domain socket connections only
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  local  all        all                              trust
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  # IPv4 local connections:
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  host    all        all        127.0.0.1/32          trust
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  # IPv6 local connections:
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  host    all        all        ::1/128              trust
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 +
by replacing the text in the last column to "trust" as it is here.  Then restart the postgresql server:
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  /etc/init.d/postgresql-8.4 restart
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Then, switch users to the "postgres" user and create a new user called "gmod":
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  su - postgres
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  createuser gmod
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    Shall the new role be a superuser? (y/n) y
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  exit  # to leave postgres user shell
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  exit  # to leave root shell
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====Install DBIx::DBStag====
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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":
 +
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  createdb test
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Then install via the cpan shell:
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  cpan
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  cpan> install DBIx::DBStag
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 +
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 ==
 
== GMOD Components ==

Revision as of 16:06, 6 June 2011

Under Construction

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
cpan> install BioPerl Bio::Graphics JSON
cpan> install Bio::Graphics::Browser2
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. 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.

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