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)
Modified qiime-uclust to strip out any fasta header text after a space because that's what SeqIO in Bio does and we do a string comparison that fails when this is not done.
Merge branch 'master' of github.com:MG-RAST/pipeline
Merge pull request #89 from jaredbischof/master

Modified qiime-uclust to strip out any fasta header text after a space
Adding wrapper to run sort and process_sims_by_source_mem from pipeline_sims_to_abundance stage script.
Created pipeline_sims_to_abundance stage script which right now just runs process_rna_sims but will also call a wrapper script to calculate protein abundances and another wrapper script to generate the abundance summary files.
Merge pull request #90 from jaredbischof/master

Adding process_rna_sims wrapper bin script and pipeline_sims_to_abundance stage script.
Forgot to initialize variables.
Merge pull request #91 from jaredbischof/master

Forgot to initialize variables.
Finished bin script that doesn't produce rna sims, but just sorts and processes them.