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Top Forums UNIX for Dummies Questions & Answers how to submit several commands together Post 302617489 by forevertl on Monday 2nd of April 2012 05:52:19 PM
Old 04-02-2012
how to submit several commands together

Dear all,

I have a simple question. I have many cut commands like below to run. I am wondering how to just type and submit all the commands at once and then each of the command will be run automaticaly one by one. Thanks a lot!

Code:
cut -d ' ' -f  3-2002          chr20_step2.mlprob>chr20_part1.mlprob   
cut -d ' ' -f  2003-4002  chr20_step2.mlprob>chr20_part2.mlprob  
cut -d ' ' -f  4003-6002  chr20_step2.mlprob>chr20_part3.mlprob   
cut -d ' ' -f  6003-8002  chr20_step2.mlprob>chr20_part4.mlprob   
cut -d ' ' -f  8003-10002  chr20_step2.mlprob>chr20_part5.mlprob   
cut -d ' ' -f  10003-12002  chr20_step2.mlprob>chr20_part6.mlprob   
cut -d ' ' -f  12003-14002  chr20_step2.mlprob>chr20_part7.mlprob   
cut -d ' ' -f  14003-16002  chr20_step2.mlprob>chr20_part8.mlprob   
cut -d ' ' -f  16003-18002  chr20_step2.mlprob>chr20_part9.mlprob   
cut -d ' ' -f  18003-20002  chr20_step2.mlprob>chr20_part10.mlprob   
cut -d ' ' -f  20003-22002  chr20_step2.mlprob>chr20_part11.mlprob   
cut -d ' ' -f  22003-24002  chr20_step2.mlprob>chr20_part12.mlprob   
cut -d ' ' -f  24003-26002  chr20_step2.mlprob>chr20_part13.mlprob   
cut -d ' ' -f  26003-28002  chr20_step2.mlprob>chr20_part14.mlprob   
cut -d ' ' -f  28003-30002  chr20_step2.mlprob>chr20_part15.mlprob   
cut -d ' ' -f  30003-32002  chr20_step2.mlprob>chr20_part16.mlprob   
cut -d ' ' -f  32003-34002  chr20_step2.mlprob>chr20_part17.mlprob   
cut -d ' ' -f  34003-36002  chr20_step2.mlprob>chr20_part18.mlprob   
cut -d ' ' -f  36003-38002  chr20_step2.mlprob>chr20_part19.mlprob   
cut -d ' ' -f  38003-40002  chr20_step2.mlprob>chr20_part20.mlprob   
cut -d ' ' -f  40003-42002  chr20_step2.mlprob>chr20_part21.mlprob   
cut -d ' ' -f  42003-44002  chr20_step2.mlprob>chr20_part22.mlprob   
cut -d ' ' -f  44003-46002  chr20_step2.mlprob>chr20_part23.mlprob   
cut -d ' ' -f  46003-48002  chr20_step2.mlprob>chr20_part24.mlprob   
cut -d ' ' -f  48003-50002  chr20_step2.mlprob>chr20_part25.mlprob   
cut -d ' ' -f  50003-52002  chr20_step2.mlprob>chr20_part26.mlprob   
cut -d ' ' -f  52003-54002  chr20_step2.mlprob>chr20_part27.mlprob   
cut -d ' ' -f  54003-56002  chr20_step2.mlprob>chr20_part28.mlprob   
cut -d ' ' -f  56003-58002  chr20_step2.mlprob>chr20_part29.mlprob   
cut -d ' ' -f  58003-60002  chr20_step2.mlprob>chr20_part30.mlprob   
cut -d ' ' -f  60003-62002  chr20_step2.mlprob>chr20_part31.mlprob   
cut -d ' ' -f  62003-64002  chr20_step2.mlprob>chr20_part32.mlprob   
cut -d ' ' -f  64003-66002  chr20_step2.mlprob>chr20_part33.mlprob   
cut -d ' ' -f  66003-68002  chr20_step2.mlprob>chr20_part34.mlprob   
cut -d ' ' -f  68003-70002  chr20_step2.mlprob>chr20_part35.mlprob   
cut -d ' ' -f  70003-72002  chr20_step2.mlprob>chr20_part36.mlprob   
cut -d ' ' -f  72003-72518  chr20_step2.mlprob>chr20_part37.mlprob


Last edited by methyl; 04-02-2012 at 07:46 PM.. Reason: please use code tags
 

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PEGASUS-RUN(1)															    PEGASUS-RUN(1)

NAME
pegasus-run - executes a workflow that has been planned using *pegasus-plan*. SYNOPSIS
pegasus-run [-Dproperty=value...][-c propsfile][-d level] [-v][--grid*][rundir] DESCRIPTION
The pegasus-run command executes a workflow that has been planned using pegasus-plan. By default pegasus-run can be invoked either in the planned directory with no options and arguments or just the full path to the run directory. pegasus-run also can be used to resubmit a failed workflow by running the same command again. OPTIONS
By default pegasus-run does not require any options or arguments if invoked from within the planned workflow directory. If running the command outside the workflow directory then a full path to the workflow directory needs to be specified. pegasus-run takes the following options -Dproperty=value The -D option allows an advanced user to override certain properties which influence pegasus-run. One may set several CLI properties by giving this option multiple times. The -D option(s) must be the first option on the command line. CLI properties take precedence over the file-based properties of the same key. See the PROPERTIES section below. -c propsfile, --conf propsfile Provide a property file to override the default Pegasus properties file from the planning directory. Ordinary users do not need to use this option unless the specifically want to override several properties -d level, --debug level Set the debug level for the client. Default is 0. -v, --verbose Raises debug level. Each invocation increase the level by 1. --grid Enable grid checks to see if your submit machine is GRID enabled. rundir Is the full qualified path to the base directory containing the planned workflow DAG and submit files. This is optional if the pegasus-run command is invoked from within the run directory. RETURN VALUE
If the workflow is submitted for execution pegasus-run returns with an exit code of 0. However, in case of error, a non-zero return value indicates problems. An error message clearly marks the cause. FILES
The following files are created, opened or written to: braindump This file is located in the rundir. pegasus-run uses this file to find out paths to several other files, properties configurations etc. pegasus.?????????.properties This file is located in the rundir. pegasus-run uses this properties file by default to configure its internal settings. workflowname.dag pegasus-run uses the workflowname.dag or workflowname.sh file and submits it either to condor for execution or runs it locally in a shell environment PROPERTIES
pegasus-run reads its properties from several locations. RUNDIR/pegasus.??????????.properties The default location for pegasus-run to read the properties from --conf propfile properties file provided in the conf option replaces the default properties file used. $HOME/.pegasusrc will be used if neither default rundir properties or --conf propertiesfile are found. Additionally properties can be provided individually using the -Dpropkey=propvalue option on the command line before all other options. These properties will override properties provided using either --conf or RUNDIR/pegasus.???????.properties or the $HOME/.pegasusrc The merge logic is CONF PROPERTIES || DEFAULT RUNDIR PROPERTIES || PEGASUSRC overriden by Command line properties ENVIRONMENT VARIABLES
PATH The path variable is used to locate binaries for condor-submit-dag, condor-dagman, condor-submit,pegasus-submit-dag, pegasus-dagman and pegasus-monitord SEE ALSO
pegasus-plan(1) AUTHORS
Gaurang Mehta <gmehta at isi dot edu> Jens-S. Vockler <voeckler at isi dot edu> Pegasus Team http://pegasus.isi.edu 05/24/2012 PEGASUS-RUN(1)
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