bhammer: support multiple libraries
bhammer: Fix exception message
spades: correctly use single end reads
Merge branch 'master' of github.com:kbase/assembly into cb
bwa: merges SAM on multiple libraries
ArastDataInputeError
bowtie2: merge SAMs on mixed reads
dynamically set bwa threads
Merge branch 'master' of github.com:kbase/assembly into cb
Merge pull request #202 from levinas/master

recipe updates
remove pipe requirement
Merge branch 'master' of github.com:kbase/assembly into cb
Merge pull request #206 from levinas/ff

MiSeq recipe and usage fix
Merge branch 'ff'
new version for rast workshop
use default queue on elm
resize quast images
update html tutorial
add appdirs
Merge branch 'master' of github.com:kbase/assembly into cb