corrected bad io handle
removed nasty bug causing fasta and fastq output to be mixed
fixed missing output of fastq data
added documention
Changed make_phylogeny to be midpoint rooted. Tested
"Start path" added in email
Added an R starter pack that makes it easy to get started with the downstream analysis
Add cp to the list of stuff that can be called several times
Merge branch 'master' of https://github.com/askerdb/qiime_pipe