Ubuntu instructions
This tutorial was written using Ubuntu Linux.
You will need about 4GB of disk space to keep the hapmap data. The main bulk of data, about 3.5GB, will reside in /var directory.
You can check your current disk usage by typing:
df -h
Downloading the data
cd ~/Desktop mkdir -p hapmap cd hapmap wget http://downloads.sourceforge.net/genedc/genepi-2007-06-20.sql.bz2 wget http://downloads.sourceforge.net/genedc/legend-2006-07.csv.bz2 bunzip2 legend-2006-07.csv.bz2
- Don’t uncompress genepi-2007-06-20.sql.bz2 (it’s a quite large file, and you don’t need in uncompressed anyway.)
Preparing database with Hapmap.org data
Please note that these instructions assume you’re working on your local machine. If you want to make an insitution-wide PostgreSQL installation, ask your network administrator how to secure it.
sudo apt-get install postgresql-8.2 sudo -u postgres createuser -s ${USER} createdb genepi -E utf-8 bzcat genepi-2007-06-20.sql.bz2 | psql genepi
You might see some messages like this, they are harmless.
ERROR: role "maciej" does not exist
The last command may take up to few hours to complete. Time of completion depends on your computer’s hard disk speed and processing power. Leaving your computer alone until it finishes, is suggested. This is one-time operation. The data will remain in the computer unless you decide to import a new release of Hapmap data. Converting your data to hapmixmap format
Installing required libraries.
sudo apt-get install build-essential libboost-dev flex bison \ libboost-filesystem-dev libboost-program-options-dev \ python-psycopg
Downloading and compiling genedc.
- Download genedc tar archive
- Compile it with usual ./configure and make
tar xfz genedc-X.Y.Z.tar.gz cd genedc-X.Y.Z ./configure make ./genedc --help
To convert your genotypes into hapmixmap format, type:
./genedc -l ../legend-2006-07.csv -i your-file
It will take about 20 seconds.
Preparing training data
From the genedc-X.Y.Z directory:
src/hapmap/cgs-hapmap -g user_genotypes.txt -o training
It will take about 30 seconds to complete the first time. Following runs will take about 5 seconds.
Last modified on Tue Feb 26 07:53:16 +0000 2008