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Welcome to the halvade wiki!

Halvade

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Hadoop Aligner & Variant Detection

Getting started

To run the program a script has been added, this reads configuration from two files:

• halvade.conf - contains configuration for the cluster / amazon EMR
• halvade_run.conf - a list of options for a DNA seq run For details on the options see the manual here. Run runHalvade.py once all options are set and wait until completion. For amazon you need to install the Amazon EMR command line interface (instructions from Amazon). For locations on s3 use this form of url: s3://bucketname/directory/to/file The emr_script option points to the location where the hadoop_bootstrap.sh is located on S3. With emr_jar the location of the Jar file (with libraries) is given on your S3 bucket.