Expected behavior

This function is expected to implement the whole logic of the aligner plugin.

Input arguments

The function receives the following arguments:

  • $1: an argument that can be used as a temporary filename
  • $2: the basename that should be used to store the sorted alignment


The function has access to the following environment variables:

Prior to GobyWeb 2.1, aligners would rely on two variables to locate a pre-installed reference sequence on the cluster node:

  • ${INDEX_DIRECTORY}: the directory were the GSNAP indexed reference has been stored on the compute node that executes the plugin.
  • ${INDEX_PREFIX}: the name of the database to search.

Since GobyWeb 2.1, these variables are been phased out in favor of reference sequence indices built with resources with artifacts. The advantage of the new mechanism is that indices can be built on request for new organisms. See the BWA_GOBY_ARTIFACT artifact for an example using resources and artifacts to install genomes and index them on demand.