Before setting up Hadoop cluster, all nodes should be configured first. It can be done by following steps in given link: http://blog.puneethabm.in/hadoop-cloudera-cluster-set-up/
Hadoop multi node cluster setup is done by following this link: http://tecadmin.net/set-up-hadoop-multi-node-cluster-on-centos-redhat/
Install CDK on Master node.
Download an active reference molecule in sdf format (say file1) against which similar shaped compounds are to be searched.
Download a chemical database of compounds in sdf format (say file2) from which structurally similar shaped compounds are to be extracted.
Make a directory ‘/data/cache/lib’ in Hadoop filesystem and copy following jar in this directory:
Copy file1 and file2 to Hadoop filesystem.
Download file ‘USR_n.jar’ and run following commands for DistMapVector (DMV) approach:
hadoop jar /path/to/USRn.jar USR.AggregateJob /path/to/file1 /path/to/file2 /path/to/output_file In this output_file is the required output.
For running via DistMapVectorLibScreen (DMVLS):
i) Download ‘lib_noreduce.jar’ and run following command for building library:
hadoop jar /path/to/USR_library.jar USR_library.AggregateJob / path/to/file2 /path/to/output_file1
ii) Download ‘screening.jar’ and run following command for final screening of compounds:
hadoop jar /path/to/screening.jar lead_compounds.AggregateJob /path/to/file1 /path/to/output_file1 /path/to/final_output_file