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README_applications

README_applications — README document, 4 kB (4518 bytes)

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March 16th, 2010

ABOUT:
------
The applications in this folder are to demonstrate the applications in 
BioScope1.2. Examples here some use human chromosome 11, 12 and some use 20 data as input and 
generally, run time for each application is couple hours long. 
(Please refer to the estimated run time section below for details).


HOW TO RUN THE APPLICATIONS:
----------------------------
 
- login as corona

- download the bioscope demo folder into /data/results/ folder of the headnode.
  It should reside only as /data/results/bioscope-<ver>/examples/applications. 
  The ini files for each application example can be found within that
  application folder.
        $cd /data/results/bioscope<ver>/examples/applications

- fix deploy location in couple of files
	1. ./examples/demos/globals/global.ini						- for all demo
	2. ./examples/applications/globals/global.ini					- for all applications
	3. ./examples/references/human_var/cnv/referenceMapping.cmap			- for cnv applications
	4. ./examples/references/human_var/cnv/referenceMapping_chr11_12.cmap		- for cnv applications
	5. ./examples/demos/cnv/referenceMapping_pe.cmap				- for cnv demo
   Each has hard coded location like /data/results/bioscope1.0/examples/demos/references/, this has tobe fixed like

	/data/results/bioscope<ver>/examples/demos/references.

	Note: The fix may be done already as part of the installation procedure


- check if the build is compatible with the system.  
        $/data/results/bioscope<ver>/examples/demos/tools/checkBuildForSGE.sh     
  if it says:  .cluster.manager.key=SGE. then it is configured for Sun grid engine
  if it says:  .cluster.manager.key=TORQUE. then it is configured for Torque
       then run following to convert TORQUE configuration to TORQUE, if you really need it.
                 $ ./tools/fixBuild_Torque_to_SGE.sh  /home/corona/bioscope
	Note: The fix may be done already as part of the installation procedure

- ./run.sh <foldername of a desired folder>
  for example:
        $ ./run.sh mappingF3.mappingF5.pairing.cnv

  This will automatically copy over the contents of mappingF3.mappingF5.pairing.cnv folder 
  into a new folder mappingF3.mappingF5.pairing.cnv.cnv.run and execute 
  the following command
	bioscope.sh .l log/example.log example.plan 
  inside the new folder.  

- ./clean.sh
  for example:
        $ ./clean.sh

  This will automatically clean all the xxx.run folders.

- The results can be seen inside the mappingF3.mappingF5.pairing.cnv.run
  folder. Typically, the mappingF3.mappingF5.pairing.cnv application has
  outputs in mappingF3.mappingF5.pairing.cnv.run/outputs directory, 
  as specified in the .ini file.

- If you create a folder <myApplication> with a plan named myApplication.plan,
  you can create a simple shell script (e.g., call run.sh) in your 
  <myApplication> folder to execute bioscope.sh for data analysis OR you can
  enter bioscope.sh at the command line.
  e.g., 
  Go to the <myApplication> folder and enter
        $ ./run.sh
        OR
        $ bioscope.sh -l log/myApplication.log myApplication.plan



ESTIMATED RUN TIME:
-------------------
The following run time was based on our Linux box with 8 processors for each of the 5 nodes.

-A- Application examples for fragment runs
(01) mapping.matobam.posErrors.diBayes - 1 hours 42 minutes 31 seconds
(02) mapping.matobam.cnv - 58 minutes 24 seconds
(03) mapping.smallIndelFrag.matobam.smallIndel - 27 minutes 53 secs
(04) wholeTranscriptome - 1 minutes 20 secs

-B- Application examples for matePair runs
(05) mappingF3.mappingR3.pairing.posErrors.diBayes - 1 hours 6 minutes 28 seconds
(06) mappingF3.mappingR3.pairing.cnv - 38 minutes 29 seconds
(07) mappingF3.mappingR3.pairing.smallIndel - 38 minutes 39 seconds
(08) mappingF3.mappingR3.pairing.largeIndel - 37 minutes 5 seconds
(09) mappingF3.mappingR3.pairing.inversion - 35 minutes 31 secs 

-C- Application examples for paired-end runs
(10) mappingF3.mappingF5.pairing.posErrors.diBayes - 20 minutes 33 seconds
(11) mappingF3.mappingF5.pairing.cnv - 26 minutes 43 seconds
(12) mappingF3.mappingF5.pairing.smallIndel - 18 minutes 1 seconds
(13) mappingF3.mappingF5.pairing.largeIndel - 17 minutes 54 seconds

-D- BioInformatics tool examples for multiple-run support
(14) tool.diBayes.multipleRuns - 44 minutes 26 seconds
(15) tool.cnv.multipleRuns - 4 minutes 29 seconds
(16) tool.smallIndel.multipleRuns - 3 minutes 30 seconds
(17) tool.largeIndel.multipleRuns - 29 seconds
(18) tool.inversion.multipleRuns - 33 seconds


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