ABCGrid supports several commands, which can be issued from AMCmaster's console window or using ABCUser.
If you use ABCUser, the command should be:
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
By default, there is a user "admin" with some FASTA files and two PDB files (under C:\master\user\admin) for testing.
will redirect output and error to file "result_and_error.out"
Besides FASTA, some other popular sequence file formats include
are also supported as the input files.
Description: Show all supported bioinformatics services
will show all supported bioinformatics services.
Description: Query the status of submitted job(s).
show information of all jobs(which submitted by current user)
show information of job which id=1
>>>j 1 2 5 7
show information of jobs which id=1,2,5 and 7.
show information of jobs which submitted by user "demo"
Description: Show connected worker nodes.
Show basic information of connected worker nodes including machine name, IP, operating system,
architecture, current status(busy, idle, etc.)
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.
kill the job which id = 1
>>>k 1 2
kill jobs which id = 1 and 2
kill jobs submitted by user 'demo'
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.
Description: Update all connected worker nodes. This is a 'admin'-only operation.
will initialize the update process.
Description: Show help message
will list supported commands.
Description: Quit ABCMaster. This is a 'admin'-only operation.
The system will ask you to confirm.