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
add deployment variable
Merge pull request #195 from kbase/ff

add deployment variable
bowtie2: merge SAMs on mixed reads
dynamically set bwa threads
Merge branch 'master' of github.com:kbase/assembly into cb
Merge pull request #198 from sebhtml/automated-tests

Automated tests
use space and no tabs for indentation in shell scripts
remove the last tab in shell scripts
modify recipes: fast, faster, rast_fast
remove tagdust from fast and faster recipes
Merge branch 'master' into ff
modify recipes; move the original 'auto' to 'smart'
add zlib path to LD_LIBRARY_PATH for rast server runtime
add paired-end check in a6 plugin and related recipes