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README_demos

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March 16th, 2010

ABOUT:
------
The demos in this folder are to demonstrate some of the applications in BioScope1.0.  Input data used is ecoli DH10B data and generally, run time for each demo is not too long (please refer to the estimated run time section below for details).


HOW TO RUN THE DEMOS:
---------------------


- 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/demos. The ini 
  files and the cmap files in the sample runs, are prepared with this  location 
  coded into it.
        $cd /data/results/bioscope-<ver>/examples/demos

- 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 to be 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 mapping

  This will automatically copy over the contents of mapping folder into a 
  new folder mapping.run and execute the following command
	bioscope.sh .l demo.log demo.plan 
  inside the new folder.  

- The results can be seen inside the mapping.run folder. Typically, the mapping 
  pipeline has outputs mapping.run/outputs/s_matching directory, as per the .ini
  file.

- Similarly, the other samples can be run,  by  running  on  the  selected desired
  folder
        $ ./run.sh something

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

  This will automatically clean all the xxx.run folders.

- demoslist

  This is the directory list that runall.sh will use to run test against.
  Make sure to update this list, if you need to use runall.sh

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

  This will automatically clean all the xxx.run folders and run the tests listed in demoslist.
  


CURRENTLY AVAILABLE DEMOS:
--------------------------
we currently have demo setups for mapping, pairing, inversion, smallIndel, largeindel, inversion, diBayes, cnv, matobam, nrbam, positionErrors, saet, wholeTranscriptome tools.
After  the  run, the  corresponding  results  can be found in  its something.run 
folders. Here is a small tabulation of its input and outputs


mapping
========
   Input: 
      reads1/*.csfasta
      reads1/*_QV.qual	
   Outputs: 
      outputs/s_matching/*.ma.*

pairing	
=======
   Input: 
      F3/ outputs/s_matching/*.ma.*
      R3/ outputs/s_matching/*.ma.*	
   Outputs: 
      MP/outputs/pairing/F3-R3-Paired.bam
      MP/outputs/pairing/F3-R3-Paired.bam.bai
      MP/outputs/pairing/pairingStats.stats
      MP/outputs/pairing/unmappedBamFile.bam
      MP/outputs/pairing/pairDistFreq

inversion
==========
   Input: 
      MP/outputs/pairing/F3-R3-Paired.bam
   Outputs: 
      MP/outputs/inversion/*

SmallIndelMP	
==========
   Input: 
      MP/outputs/pairing/F3-R3-Paired.bam
      MP/outputs/pairing/F3-R3-Paired.bam.bai
	
   Outputs: 
      MP/outputs/smallIndel/*

SmallIndelFrag(plus smallIndel)
==========
   Input:
      outputs/s_mapping/*.ma.*
   Outputs:
      outputs/smallindel/*

cnv
==========
   Input:
      outputs/pairing/F3-F5-P2-Paired.bam
      outputs/pairing/F3-F5-P2-Paired.bam.bai  
   Outputs:
      outputs/cnv/*
 
diBayes:
==========
   Input:
      outputs/pairing/F3-R3-Paired.bam
      outputs/position-errors/F3-R3-Paired_F3_positionErrors.txt
      outputs/position-errors/F3-R3-Paired_R3_positionErrors.txt
   Output:
      outputs/diBayes/*

wholeTranscriptome:
==========
   Input:
      reads/HBR.chr17_6.100k.mixed.F3.csfasta  
      reads/HBR.chr17_6.100k.mixed.qual
      references/human_chr17_6.exons.gtf  
      references/human_filter_reference.fasta
      references/human_chr17_6.fa
   Output:
      outputs/single_read/counttag  
      outputs/single_read/mapping
      outputs/single_read/sam2wig

wholeTranscriptomePE:
==========
   Input:
      reads/f3/F3.csfasta
      reads/f3/F3.qual
      reads/f5/F5.csfasta
      reads/f5/F5.qual
      references/human_chr17_6.exons.gtf
      references/human_chr17_6.fa
      references/human_chr17_6.properties
      references/human_filter_reference.fasta
   Output:
      outputs/paired_end/counttag
      outputs/paired_end/junction_finder
      outputs/paired_end/mapping

      outputs/paired_end/sam2wig

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

(01) saet - 4 seconds
(02) mapping - 1 minute 9 seconds
(03) pairing - 4 minutes 33 seconds
(04) matobam - 16 seconds
(05) positionErrors - 20 seconds
(06) diBayes - 4 minutes 34 seconds
(07) cnv - 3 minutes 34 seconds
(08) smallIndelFrag - 31 seconds
(09) smallIndelMP - 14 minutes 32 seconds
(10) largeIndel - 13 seconds
(11) inversion - 5 seconds
(12) wholeTranscriptome - 1 minutes 19 seconds
(13) wholeTranscriptomePE - 2 minutes
  


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