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Tutorial: GotCloud (view source)

Revision as of 10:51, 22 February 2013

44 bytes added ,  10:51, 22 February 2013
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== STEP 1 : Setup GotCloud ==
 
== STEP 1 : Setup GotCloud ==
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 +
=== Step 1c: Setup Environment ===
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To facilitate running this tutorial, set environment variables:
 +
* GCHOME to the path to the base directory of your gotcloud instalation
 +
* GCDATA to the path to the base directory of the example data instalation
 +
In the instructions below, we
 +
 +
First check your shell using:
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  ps -p $$ -ocomm=
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 +
For bash, sh:
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export GCHOME=~/gotcloud
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export GCDATA=~/gotcloudExample
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export GCOUT=~/gotcloudTutorial
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For csh, tcsh:
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setenv GCHOME ~/gotcloud
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setenv GCDATA ~/gotcloudExample
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setenv GCOUT ~/gotcloudTutorial
    
=== Step 1a: Install GotCloud ===
 
=== Step 1a: Install GotCloud ===
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Otherwise, you can install it in your own directory:
 
Otherwise, you can install it in your own directory:
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# Change directory to where you want to install gotcloud
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# Create & Change directory to where you want to install gotcloud
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# Download the gotcloud tar from TBD
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# Download the gotcloud tar from the ftp site.
 
# Extract the tar
 
# Extract the tar
 
# Build the source
 
# Build the source
   −
  cd ~                    # Move to your home directory (or wherever you want to install)
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  mkdir -p $GCHOME; cd $GCHOME
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  wget TBD                # Download
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  wget ftp://share.sph.umich.edu/gotcloud/gotcloud.tar  # Download
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  tar xvf gotcloud.tar   # Extract
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  tar xvf gotcloud.tar --strip 1  # Extract
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  cd gotcloud/src; make   # Build source
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  cd $GCHOME/src; make           # Build source
 
   
 
   
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The example dataset we'll be using is included in this tar-ball TBD.
 
The example dataset we'll be using is included in this tar-ball TBD.
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# Change directory to where you want to install the example dataset
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# Create & Change directory to where you want to install the Tutorail data
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# Download the dataset tar from TBD
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# Download the dataset tar from the ftp site
 
# Extract the tar
 
# Extract the tar
   −
  cd ~                          # Move to your home directory (or wherever you want to install)
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  mkdir -p $GCDATA; cd $GCDATA
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  wget TBD                      # Download
+
  wget ftp://share.sph.umich.edu/gotcloud/gotcloudExample.tar  # Download
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  tar xvf gotcloudExample.tar   # Extract
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  tar xvf gotcloudExample.tar --skip 1  # Extract
   −
=== Step 1c: Setup Enviornment for Testing ===
  −
To facilitate running this tutorial, set environment variables:
  −
* GCHOME to the path to the base directory of your gotcloud instalation
  −
* GCDATA to the path to the base directory of the example data instalation
  −
In the instructions below, we
  −
  −
First check your shell using:
  −
  ps -p $$ -ocomm=
  −
  −
For bash, sh:
  −
export GCHOME=~/gotcloud/
  −
export GCDATA=~/gcTutorial/
  −
  −
For csh, tcsh:
  −
setenv GCHOME ~/gotcloud/
  −
setenv GCDATA ~/gcTutorial/
      
== STEP 2 : Run GotCloud Alignment Pipeline ==
 
== STEP 2 : Run GotCloud Alignment Pipeline ==
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Run the mapping pipeline:
 
Run the mapping pipeline:
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  $GCHOME/gen_biopipeline.pl --conf $GCDATA/[[GBR60map.conf]] --out_dir mappingResults
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  $GCHOME/gotcloud align --conf $GCDATA/[[GBR60map.conf]] --outdir $GCOUT
    
TBD - add link explaining the contents of the .conf & .index files.
 
TBD - add link explaining the contents of the .conf & .index files.
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/6497"

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