Installation manual

Step 1: Installation of prerequisites on your Local System:

A. Software:
On your local system, you will need to install:

• Python-2.6 or greater
  
• Wget (latest version)
  
• Java (JDK latest version)
  Permanently set the environment variables in the my.bashrc file:
      export JAVA_HOME=$JAVA_INSTALLATION_DIRECTORY
      PATH=$PATH: :$JAVA_INSTALLATION_DIRECTORY/bin
  
  For example:
      export JAVA_HOME=$JAVA_INSTALLATION_DIRECTORY
      PATH=$PATH:$JAVA_INSTALLATION_DIRECTORY/bin
  
  
B. Cloud:
PathSeq uses Amazon Web Services (AWS) to perform computation in the cloud. Therefore, to use Pathseq, you will need an AWS account and you will need to pay for the AWS resource time. If you do not already have an AWS account, register at AWS for a new account. Note that you will need credit card information to enable your Amazon account.
If you have difficulties with the Amazon setup, please consult the Amazon documentation and resources.

Step 2: Installation of Ec2-api-tools on your Local System

1. Download Ec2-api-tools from here.
2. Extract the zip file.
   unzip ec2-api-tools-xxxxxx.zip
3. Permanently set the environment variables in the my.bashrc file. Replace Xs and paths with the information noted in the previous step.
   export EC2_HOME=$LOCAL_DIRECTORY/ec2-api-tools-xxxxxx
    export EC2_AMITOOL_HOME=$LOCAL_DIRECTORY/ec2-api-tools-xxxxxx
    Add to path: $LOCAL_DIRECTORY/ec2-api-tools-xxxxxx/bin

    For example: (edit ~/.my.bashrc)
    export EC2_HOME=$LOCAL_DIRECTORY/ec2-api-tools-xxxxxx
    export EC2_AMITOOL_HOME=$LOCAL_DIRECTORY/ec2-api-tools-xxxxxx
    PATH=$PATH:$LOCAL_DIRECTORY/ec2-api-tools-xxxxxx/bin

Note: Make sure that these variables are set correctly in your environment before proceeding.

4. Download the Access key ID, Secret access key, important information to be downloaded onto your Local System

Note: In this Step, please note down the Amazon account information which will be used in the later steps of installation.

5. Use source command to set the environment of the local system with the new variables.
   source ~/.my.bashrc

6. Authorize ports 22 and 60 for transfer and access the cloud.
   ec2-authorize default -p 22
   ec2-authorize default -p 60

Step 3: Install the S3cmd tool from http://s3tools.org/s3cmd (refer to s3cmd website for detailed installation instructions):

   1. python setup.py install
   2. s3cmd --configure

NOTE: Your AWS account information is required for this step.

Step 4: Optional: If you want to request an increase to your instance limit (i.e. Amazon allocates EC2 clusters with up to 20 nodes total (includes 1 master node) by default). To work with more nodes, fill out the form on this page:
            http://aws.amazon.com/contact-us/ec2-request
Amazon representative my help you in this process, please speak to one of them.

Step 5: Installation of PathSeq
Note: Please make sure that your configured the cluster.config file with correct information before proceeding to Step 6

Step 6: Building your own PathSeq Amazon machine image

1. Change the permission of C-shell scripts in $LOCAL_DIRECTORY/PathSeq directory
   chmod 777 *.com

2. Build your own Amazon machine image using create_ownAMI.com script    $LOCAL_DIRECTORY/PathSeq/create_ownAMI.com

3. Please follow the instructions on the screeen.

4. After successfully building the Image, Please login into your Amazon Web Services account to check whether the instance has been terminate or not.

For example: (Final statments that indicates successful completion are as follows)
..............................
Bundle upload completed.
Done
IMAGE ami-0434c36d
Terminate with: ec2-terminate-instances i-14980879
Creation completed

Note: Storing the image in the S3 bucket costs very nominal amount.