"baseCommand": "ls",
"arguments": [{"valueFrom": "$(runtime.outdir)"}]
})
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
}],
"baseCommand": "ls"
}
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosCommandTool(runner, tool, work_api="jobs", avsc_names=avsc_names,
make_fs_access=make_fs_access, loader=Loader({}))
arvtool.formatgraph = None
'runtime_constraints': {
'docker_image': 'arvados/jobs',
'min_cores_per_node': 3,
- 'min_ram_mb_per_node': 3000,
+ 'min_ram_mb_per_node': 3512, # ramMin + keep_cache
'min_scratch_mb_per_node': 5024, # tmpdirSize + outdirSize
'keep_cache_mb_per_task': 512
}
mockcollection().portable_data_hash.return_value = "99999999999999999999999999999999+118"
- make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess, api_client=runner.api)
+ make_fs_access=functools.partial(arvados_cwl.CollectionFsAccess,
+ collection_cache=arvados_cwl.CollectionCache(runner.api, None, 0))
arvtool = arvados_cwl.ArvadosWorkflow(runner, tool, work_api="jobs", avsc_names=avsc_names,
basedir="", make_fs_access=make_fs_access, loader=document_loader,
makeTool=runner.arv_make_tool, metadata=metadata)