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.
Finished with stage script that runs a single bin script "sims_to_abundance" which processes aa and rna sims and produces abundance summaries.  All the "work" except for moving files around is now performed inside the bin scripts instead of having a lot of the processing in the load stage (pipeline_loadDB) as before.
Finished with bin script that processes aa and rna sims and takes a lot of the work out of the pipeline_loadDB script.  This script takes as primary input the aa and rna sims and cluster files and outputs the abundance summary files, the filter.seq file and the source.stats file.
Merge pull request #92 from jaredbischof/master

Finished and tested a few scripts for recompute and awe.
Changed check for the "assembled" option in the Job database to check for the existence of the $raw_dir/$job_num.abundance file because the recompute cluster can't see the Job database.
Created separate Pipeline library for the recompute that will print sql statements to a file in the jobsv3 directory of the job that is being recomputed because it cannot access the Job database directly from the recompute cluster.
Edited stage script to use Pipeline_recompute.pm instead of Pipeline.pm.
Merge pull request #93 from jaredbischof/master

Updates for recompute.
Fixed variable name.
Merge pull request #94 from jaredbischof/master

Fixed variable name.
Minor fix for recompute.
Merge pull request #95 from jaredbischof/master

Minor fix for recompute.