src/toil/lib/aws/__init__.py | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

---

src/toil/cwl/cwltoil.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix exception checking for exit_code

requirements-cwl.txt | 2 1 + 1 - 0 !
src/toil/version.py | 12 12 + 0 - 0 !
2 files changed, 13 insertions(+), 1 deletion(-)

 fixing version.py that is variable and required

requirements-cwl.txt | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 skip galaxy-lib, not yet packaged for debian

docs/gettingStarted/quickStart.rst | 91 35 + 56 - 0 !
docs/index.rst | 1 0 + 1 - 0 !
2 files changed, 35 insertions(+), 57 deletions(-)

 update docs to reflect a local install

requirements.txt | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 skip addict

requirements.txt | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 allow for use of python3-docker package

setup.py | 7 2 + 5 - 0 !
1 file changed, 2 insertions(+), 5 deletions(-)

 ship all of the tests and supporting data

requirements.txt | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 skip the py-tes dependency

src/toil/jobStores/fileJobStore.py | 17 10 + 7 - 0 !
1 file changed, 10 insertions(+), 7 deletions(-)

 os.link does not work with debci based setup and hence default to atomic copy
 when it does not work as intended

docs/appendices/deploy.rst | 14 7 + 7 - 0 !
docs/contributing/contributing.rst | 2 1 + 1 - 0 !
docs/gettingStarted/install.rst | 2 1 + 1 - 0 !
docs/gettingStarted/quickStart.rst | 22 11 + 11 - 0 !
docs/running/cliOptions.rst | 4 2 + 2 - 0 !
docs/running/cloud/amazon.rst | 6 3 + 3 - 0 !
docs/running/cloud/clusterUtils.rst | 4 2 + 2 - 0 !
docs/running/cloud/gce.rst | 4 2 + 2 - 0 !
8 files changed, 29 insertions(+), 29 deletions(-)

 make sure the doc applies to debian installations with python3

src/toil/jobStores/aws/utils.py | 9 5 + 4 - 0 !
1 file changed, 5 insertions(+), 4 deletions(-)

 avoid an unnecessary mypy_boto3_s3 import

src/toil/test/src/helloWorldTest.py | 2 1 + 1 - 0 !
src/toil/test/src/realtimeLoggerTest.py | 2 1 + 1 - 0 !
src/toil/test/src/userDefinedJobArgTypeTest.py | 2 1 + 1 - 0 !
3 files changed, 3 insertions(+), 3 deletions(-)

 tests: only request a single core
Bugs: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1031192