DAMIAN was developed for an employment in Linux environments. It is known to run with CentOS / Red Hat Enterprise Linux and Ubuntu. It likely works well with other Linux distributions. However, all examples listed here are written and tested only for CentOS 7. Installation may be different on other distributions and you may have to make minor modifications (for example some packages may need to be installed additionally (like curl or Ruby), you may need to replace 'yum' with 'apt-get' or the names of packages may differ between distributions).
DAMIAN is written in Ruby, which is very likely already installed on your system. You can verify that with:
ruby --version
Additionally you will need to have Perl and a JAVA runtime environment installed. Again, it is very likely already installed on your system and you may not need to do anything. You can verify that with:
perl --version java -version
A PostgreSQL database system is required to run DAMIAN. We do not cover the required setup steps here, because many other sites provide well written tutorials. They will guide you through the few required steps within minutes.
Once the database system is installed, create a new user and database. For example:
CREATE USER damian_user WITH PASSWORD 'my_password'; CREATE DATABASE damian_db WITH OWNER damian_user;
Additionally, you will need to install development header files for Ruby and Postgres as well as Perl dependencies :
yum install ruby-devel postgresql-devel perl-core perl-JSON perl-Digest-MD5 -y
Next we will install a gem which allows Ruby to interact with PostgreSQL:
gem install pg -v 0.19
Since we are already at it, we will add another gem which will allow Ruby to write files in a well known spread sheet format:
gem install nokogiri -v 1.6.8.1
gem install axlsx
And finally one for pattern matching:
gem install amatch
DAMIAN depends on the following third party software (it does not need to be installed manually):
DAMIAN comes with a (minimally modified) version of IDBA_UD and the other software can be installed automatically using the download_dependencies.sh script in the 3rd_party folder.
sh 3rd_party/download_dependencies.sh
The script uses the program curl, which should be installed already on most systems. If not, you can either choose to install it or change the script to use other tools (like wget). If you prefer to install the software manually, please set the paths in config.rb accordingly.
Next you should execute the getall.sh script in the database subfolder:
sh databases/get_all.sh
This script will download several (huge) reference databases. Please be patient, as it may take a very long time.
Briefly check the file config.rb and make sure that the details given in the DATABASE section are correct. Please do not make any other changes to this file at this point.
To populate DAMIAN's internal database, please execute the following command:
ruby damian_database.rb --erase_and_rebuild --names databases/tax/names.dmp --nodes databases/tax/nodes.dmp --hmm databases/pfam/Pfam-A.hmm.txt --taxdepth databases/pfam/pfamA_tax_depth.txt
The file ~/.ncbirc can be created automatically during the installation process. If you want to create or edit it manually, make sure its content looks similar to this:
[BLAST] BLASTDB=/home/mlk/damian/databases/blast
Wiki: Analyzing individual samples
Wiki: Home
Wiki: Managing host organisms
Wiki: Verifying the installation