Beta support for configurable dependency resolution & Biocontainers.#214

Merged

mr-c merged 23 commits intocommon-workflow-language:masterfrom jmchilton:galaxy_deps

Jul 7, 2017

+4,094-14

Commits on Jul 7, 2017

Beta support for configurable dependency resolution & Biocontainers.
jmchilton
committed
galaxy-lib as a setup.py plugin
jmchilton
committed
Implement and add example for specifications in SoftwareRequirements.
jmchilton
committed
Fix --no-container, add example combining Conda + explicit docker options.
jmchilton
committed
Fix whitespace deleted in previous rebase.
jmchilton
committed
Fixup seqtk seq example w/wrong name.
jmchilton
committed
Example using environment-like modules.
jmchilton
committed
Fix Python 3 incompatibility in PYTHON_RUN_SCRIPT.

jxtx
authored and
jmchilton
committed
Fix stderr/stdout handling in external bash script processing of jobs.
jmchilton
committed
Sorry for the XML - we didn't need to do that.
jmchilton
committed
Demonstrate mapping of SoftwareRequirements to local resources.
jmchilton
committed
Updated typeshed defs for Galaxy-lib?
jmchilton
committed
E251, E241

mr-c
authored and
jmchilton
committed
E261

mr-c
authored and
jmchilton
committed
add default value for find_default_container

mr-c
authored and
jmchilton
committed
Update job.py

mr-c
authored and
jmchilton
committed
Fix null handling in redone find_default_container usage.
jmchilton
committed
Refine type signatures a bit for galaxy-lib.
jmchilton
committed
Refactor utilities for dealing with SoftwareRequirements into own module.
jmchilton
committed
Furter refine type descriptions for galaxy-lib.
jmchilton
committed
I suppose this is needed after 0b6f27e.
jmchilton
committed
Docs for resolving SoftwareRequirements.
jmchilton
committed
Merge branch 'master' into galaxy_deps
mr-c
authored

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Beta support for configurable dependency resolution & Biocontainers.#214

Commits on Jul 7, 2017

Beta support for configurable dependency resolution & Biocontainers.

galaxy-lib as a setup.py plugin

Implement and add example for specifications in SoftwareRequirements.

Fix --no-container, add example combining Conda + explicit docker options.

Fix whitespace deleted in previous rebase.

Fixup seqtk seq example w/wrong name.

Example using environment-like modules.

Fix Python 3 incompatibility in PYTHON_RUN_SCRIPT.

Fix stderr/stdout handling in external bash script processing of jobs.

Sorry for the XML - we didn't need to do that.

Demonstrate mapping of SoftwareRequirements to local resources.

Updated typeshed defs for Galaxy-lib?

E251, E241

E261

add default value for find_default_container

Update job.py

Fix null handling in redone find_default_container usage.

Refine type signatures a bit for galaxy-lib.

Refactor utilities for dealing with SoftwareRequirements into own module.

Furter refine type descriptions for galaxy-lib.

I suppose this is needed after `0b6f27e`.

Docs for resolving SoftwareRequirements.

Merge branch 'master' into galaxy_deps