Merge pull request #81 from jaredbischof/master

Fixed parallel clustering to provide unique cluster ID's
Merge pull request #82 from jaredbischof/master

Fixing temp filename.
update in awe_blat.py: multi-threading and sort in pwd
Merge pull request #83 from wtangiit/master

update in awe_blat.py
Merge pull request #84 from jaredbischof/master

Fixed bugs, added comments, and made more readable process_clusters script.
add awe_rna_search.pl, awe wrapper for mg-rast stage 425
add awe_rna_blat.pl, awe wrapper for mg-rast stage 440
Merge pull request #85 from wtangiit/master

add awe wrappers for RNA related stages
add awe_rna_blat.sh, an alternate wrapper for stage 450 (blat+sort)
Merge pull request #86 from wtangiit/master

add awe_rna_blat.sh, an alternate wrapper for stage 450 (blat+sort)
add awe_annotate.pl, awe wrapper for mg-rast stage 650 and part of 450
Merge pull request #87 from wtangiit/master

add awe_annotate.pl (awe wrapper for stage 650 and part of 450)
awe_annotate.pl add output prefix as a command line option
Merge branch 'master' of https://github.com/MG-RAST/pipeline
add wrapper awe_parallel_clust.pl for stage 440 and 550
Merge pull request #88 from wtangiit/master

awe wrapper for parallel_cluster (used by stage 440, 550)
Merge branch 'master' of github.com:MG-RAST/pipeline