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Beta support for configurable dependency resolution & Biocontainers. #214

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merged 23 commits into from
Jul 7, 2017
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85158a3
Beta support for configurable dependency resolution & Biocontainers.
jmchilton Oct 18, 2016
ee83315
galaxy-lib as a setup.py plugin
jmchilton Jun 27, 2017
1e6ea02
Implement and add example for specifications in SoftwareRequirements.
jmchilton Jun 27, 2017
ef3e6f2
Fix --no-container, add example combining Conda + explicit docker opt…
jmchilton Jun 27, 2017
432ad4c
Fix whitespace deleted in previous rebase.
jmchilton Jun 27, 2017
e7059a2
Fixup seqtk seq example w/wrong name.
jmchilton Jun 27, 2017
913f617
Example using environment-like modules.
jmchilton Jun 27, 2017
6b929f1
Fix Python 3 incompatibility in PYTHON_RUN_SCRIPT.
jxtx Jun 27, 2017
79bae7d
Fix stderr/stdout handling in external bash script processing of jobs.
jmchilton Jun 27, 2017
b19f60d
Sorry for the XML - we didn't need to do that.
jmchilton Jun 27, 2017
461b10f
Demonstrate mapping of SoftwareRequirements to local resources.
jmchilton Jun 27, 2017
368f888
Updated typeshed defs for Galaxy-lib?
jmchilton Jun 27, 2017
02ecac6
E251, E241
mr-c Jun 29, 2017
a55aee1
E261
mr-c Jun 29, 2017
0823ce8
add default value for find_default_container
mr-c Jun 29, 2017
3ed134d
Update job.py
mr-c Jun 29, 2017
15a6ab4
Fix null handling in redone find_default_container usage.
jmchilton Jul 3, 2017
dac661e
Refine type signatures a bit for galaxy-lib.
jmchilton Jul 3, 2017
0b6f27e
Refactor utilities for dealing with SoftwareRequirements into own mod…
jmchilton Jul 3, 2017
d473e3a
Furter refine type descriptions for galaxy-lib.
jmchilton Jul 3, 2017
75c8d81
I suppose this is needed after 0b6f27e83064e80b6a2ce21f9a3d2be3f21cba9f.
jmchilton Jul 7, 2017
5522e88
Docs for resolving SoftwareRequirements.
jmchilton Jul 7, 2017
fd2ac01
Merge branch 'master' into galaxy_deps
mr-c Jul 7, 2017
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Furter refine type descriptions for galaxy-lib.
jmchilton committed Jul 7, 2017

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commit d473e3a1e6e337568d367a4f359f3d0a88272c41
4 changes: 3 additions & 1 deletion cwltool/software_requirements.py
Original file line number Diff line number Diff line change
@@ -7,8 +7,10 @@
ways to adapt new packages managers and such as well.
"""

import argparse
import os
import string
from typing import (Any, Dict, List, Text)

try:
from galaxy.tools.deps.requirements import ToolRequirement, ToolRequirements
@@ -72,7 +74,7 @@ def build_job_script(self, builder, command):


def get_dependencies(builder):
# type: (Any) -> List[ToolRequirement]
# type: (Any) -> ToolRequirements
(software_requirement, _) = get_feature(builder, "SoftwareRequirement")
dependencies = [] # type: List[ToolRequirement]
if software_requirement and software_requirement.get("packages"):
2 changes: 1 addition & 1 deletion typeshed/2.7/galaxy/tools/deps/__init__.pyi
Original file line number Diff line number Diff line change
@@ -12,7 +12,7 @@ from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver as T
log = ... # type: Any
CONFIG_VAL_NOT_FOUND = ... # type: Any

def build_dependency_manager(config): ...
def build_dependency_manager(config: Any) -> DependencyManager: ...

class NullDependencyManager:
dependency_resolvers = ... # type: Any
6 changes: 3 additions & 3 deletions typeshed/2.7/galaxy/tools/deps/requirements.pyi
Original file line number Diff line number Diff line change
@@ -13,10 +13,10 @@ class ToolRequirement:
version = ... # type: Any
specs = ... # type: Any
def __init__(self, name: Optional[Any] = ..., type: Optional[Any] = ..., version: Optional[Any] = ..., specs: Any = ...) -> None: ...
def to_dict(self) -> Dict[Any]: ...
def to_dict(self) -> Dict[str, Any]: ...
def copy(self): ...
@staticmethod
def from_dict(dict: Dict[Any]) -> ToolRequirement: ...
def from_dict(dict: Dict[str, Any]) -> ToolRequirement: ...
def __eq__(self, other): ...
def __ne__(self, other): ...
def __hash__(self): ...
@@ -31,7 +31,7 @@ class RequirementSpecification:
def short_name(self): ...
def to_dict(self): ...
@staticmethod
def from_dict(dict: Dict[Any]) -> ToolRequirements: ...
def from_dict(dict: Dict[str, Any]) -> ToolRequirements: ...
def __eq__(self, other): ...
def __ne__(self, other): ...
def __hash__(self): ...