General :: Simultaneously Execute 8 Instances Of A Program Until All Input Files Are Processed?

Sep 27, 2010

I have a machine with 8 cores. I have a directory of input files that I need to process using a non-parallelized program. I would like to write a script that works its way through a list of commands executing 8 commans (i.e., instances of this program; each with specific flags having to do with the current input file) until the list of commands has been exhausted. Is there an easy way to do this?

Code:

hamstrsearch_local-hmmer3.pl -protein -refspec=lotgi_2713 -hmmset=lophotrochozoa_hmmer3 -sequence_file=Aplysia_californica.fas -taxon=ACAL

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Programming :: Awk - Input From One Line - Execute Program - Input From Next Line - Execute Program

Sep 25, 2010

I have a file with two fields of numbers that I want to use as input for another program.

Code:

The above code does not work, as I think it would take the whole first and second fields as the input for one particular instance of the program 'inputbashangle'. What I want is to get the first two numbers from the first line of the file 'outfailtest', execute 'inputbashangle' with them, then move on to the first two numbers of the second line for all the lines of 'outfailtest'.

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I have bees assigned a problem which states that :

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Here is the code:

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May 15, 2010

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cat abc.txt | ~/test/rubysrc/foo.rb

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The button identifies as

Bus 001 Device 035: ID 1130:600d Tenx Technology, Inc.

I'd like to know if there's either

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General :: Deleting Files On USB - Input / Output Error

May 4, 2009

[root@localhost media]# ls UMESH
[root@localhost media]# cd UMESH/
[root@localhost UMESH]# ll
ls: cannot access ejb: Input/output error
total 0 d? ejb
[root@localhost UMESH]# rm -rf ejb
rm: cannot remove 'ejb': Input/output error
[root@localhost UMESH]# ll
ls: cannot access ejb: Input/output error
total 0 d? ejb
[root@localhost UMESH]#

The privileges for root for UMESH are as below:
[root@localhost media]# ll
total 4
drwxr-xr-x 3 vickey root 4096 1970-01-01 05:30 UMESH
[root@localhost media]#

Also I can't even paste a file in the USB.

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Apr 24, 2011

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May 18, 2011

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Jun 23, 2010

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General :: Shell Scripting: Getting Multiple Input Files For An Application?

Sep 21, 2010

I am running an application called QuantiSNP [URL]. The binary file is "quantisnp2", called upon in the "run_quantisnp2.sh" supplied by the authors. I am only able to run the application for single file processing (e.g. 1 input file for 1 sample; I can't run the batch file processing because I don't have the necessary BeadStudio report files, which has different formatting for the input files).

The difficulty is that I have 300 samples (300 unique sample IDs) and 3 input files for each sample for a total of 900 runs of this application. I am wondering how would I be able to automate this process as a shell script instead of basically manually changing the sample ID and respective input files every time a run completes? I bolded the single file processing shell script command line options below that need to be changed for each sample/input single file processing run. The command line option "--sampleid" is for the name given to the processed output files corresponding to the sample of interest and there are 3 input files for each sample.

/home2/jason/QuantiSNP/quantisnp/linux64/run_quantisnp2.sh /home2/jason/QuantiSNP/MCR/v79/ --config /home2/jason/QuantiSNP/quantisnp/config/params.dat --levels /home2/jason/QuantiSNP/quantisnp/config/levels-affy.dat --outdir /home2/jason/QuantiSNP/quantisnp_out/ --sampleid sample1 --gender female --input-files /home2/jason/files/sample1_input.txt

Note that each sample has 3 input files, for a total of 3 runs of "quantisnp2" for each sample. e.g.

SAMPLEID INFILE
sample1 /home2/jason/files/sample1_input.txt
sample1 /home2/jason/files/sample1_input2.txt
sample1 /home2/jason/files/sample1_input3.txt

[code]....

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