bhammer: support multiple libraries
bhammer: Fix exception message
spades: correctly use single end reads
Merge branch 'master' of github.com:kbase/assembly into cb
fix indentation in test

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
use a repository and a branch for testing

Link: https://github.com/kbase/assembly/issues/188
Link: https://github.com/kbase/assembly/issues/189
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
run summarize_test for arast.t

Link: https://github.com/kbase/assembly/issues/187
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
add endpoint information

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
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
fix code using the status of a job

Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
fix binary blob in automated test

Link: https://github.com/kbase/assembly/issues/197
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
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