ABCGrid supports several commands, which can be issued from AMCmaster's console window or using ABCUser. If you use ABCUser, the command should be:

>/JAVA_HOME/bin/java -jar user.jar [command]

If you use ABCMaster's console window:


We give examples by using ABCMaster's console window.

  1. Run

    Syntax:r command [params]

    Description: Run a job


    >>>r blastall -p blastp -i pdb_100.fasta -d nr -o pdb_100.blastp -m 9

    will run a blastp search again nr database using input sequence file pdb_100.fasta.
    >>>r CE - pdbdemo1.ent A pdbdemo2.ent A scratch

    will run a CE structure alignment between chain A of pdbdemo1.ent and chain B of pdbdemo2.ent.

    Output and error redirection are also supported:

    >>>r CE - pdbdemo1.ent A pdbdemo2.ent A scratch 1>abc

    will redirect output to file "abc".
    Note: By defult, the output of CE is "screen". To get the result in a file, you should always use redirection. So does the hmmpfam.
    >>>r hmmpfam Pfam_ls input.seq 1>result.out 2>result.err

    will redirect output to file 'result.out' and error to file 'result.err'.
    >>>r hmmpfam Pfam_ls input.seq >result_and_error.out

    will redirect output and error to file "result_and_error.out"
    By default, there is a user "admin" with some FASTA files and two PDB files (under C:\master\user\admin) for testing.

    Besides FASTA, some other popular sequence file formats include EMBL, Genbank, SwissProt, PDB, are also supported as the input files.

  2. Service


    Description: Show all supported bioinformatics services



    will show all supported bioinformatics services.
  3. Job

    Syntax:j [job_id]

    Description: Query the status of submitted job(s).



    show information of all jobs(which submitted by current user)
    >>>j 1

    show information of job which id=1
    >>>j 1 2 5 7

    show information of jobs which id=1,2,5 and 7.
    >>>j demo

    show information of jobs which submitted by user "demo"
  4. Worker


    Description: Show connected worker nodes.



    Show basic information of connected worker nodes including machine name, IP, operating system, architecture, current status(busy, idle, etc.)
  5. Kill

    Syntax:k [job_id] [user]

    Description: Kill a job. A User can only kill his jobs. If a User is administrator (which group is "admin"), he can kill any jobs.


    >>>k 1

    kill the job which id = 1
    >>>k 1 2

    kill jobs which id = 1 and 2
    >>>k demo

    kill jobs submitted by user 'demo'
    >>>k 0

    kill all jobs submitted by current user. value 0 indicate all jobs. If you are 'admin', this will kill all jobs submitted by all user.
  6. Update


    Description: Update all connected worker nodes. This is a 'admin'-only operation.



    will initialize the update process.
  7. Help


    Description: Show help message



    will list supported commands.
  8. Quit


    Description: Quit ABCMaster. This is a 'admin'-only operation.



    The system will ask you to confirm.


2006 Center for Bioinformatics, Peking University.

Last Update

Dec 25 2006