gjospin/Amphora-2 — Issue #67: smaller filesystem footprint / stream processing
Author: koadman
Created: 2012-02-02 05:35:58+00:00
State: open

right now amphora2 stores an enormous amount of data on the disk, creating several files that are probably unnecesary:

1. it creates a copy of the marker genes in the output directory, these could be read from the marker path (though there are shared storage situations where copying to a local storage device could speed computation)

2. it stores the blast/rapsearch output on disk, however this file is immediately processed to create marker candidates and could instead be read in as a pipe directly from blast/rapsearch.

3. same issue for hmmscan

4. there are several transient files in aligndir that need not be kept