This shows how to submit a job an EMR (Elastic Map Reduce) cluster on AWS to get id
Notes
This command has 2 modes (Hadoop, regular),
Warning
Multi-fasta files have to formatted before passing them as inputs. Please check input Formatter.
>>> ./EHPC-EMR --submit -d=DOMAIN --command=COMMAND OPTIONS
All parameters should be in format parameter=value
--mode, -m mode of the job, either [Hadoop, regular], default regular
Note: in Hadoop mode, HPC-cloud converts the command and input for a Hadoop streaming Job
in regular mode, HPC-cloud passes the job as a classic job which the tool will handle hadoop
--command original command to run
--input-files, -i list of input files seprated by commas
--output-files, -o list of expected output files seprated by commas
--domain, -d Domain of the main node
--cache-files, -cf list of cache files to cache to mappers and reducers, for hadoop mode only
--cache-archives, -ca list of cache archives to cache to mappers and reducers, for hadoop mode only
--files list of files to pack with the job
--reducer path of the reducer to execute e.g 'cat', default NONE
--output-dir path of the output dir for the mappers and reducers, default /home/hadoop/output/ID
--conf set of hadoop configuration parameters seprated by commas, for hadoop mode only
--owner the owner of job
if owner is system, the commad will execute on the command line, client will wait the job is Done
if owner is hadoop, the job will be submitted as a Hadoop job
if owner is otherwise, this will be a PBS Torque Job
--no-fetch-output-files Don't fetch output files
Example 1
Run blast of a query file ‘query.1000.formatted’ against est_human db copied in Example 1 on ec2......com
./EHPC-EMR --submit --mode=hadoop -d=ec2......com -id=1 --command='./blastn -query /home/hadoop/query.1000.formatted -db est_human/est_human -out /home/hadoop/blast/out.blast' --input-files='s3://eg.nubios.us/emr/query.1000.formatted' --output-files='/home/hadoop/blast/out.blast' --output-dir='/home/hadoop/output/1' --reducer=NONE -ca=hdfs:///home/hadoop/dbs/est_human.tar.gz#est_human -cf=s3://eg.nubios.us/emr/blastn.64#blastn --conf=mapred.reduce.tasks=1,mapred.map.tasks=1
Returns JOBID