example doesn't run out of the box
AMChalkie opened this issue · 1 comments
example doesn't run out of the box
Running in examples directory gives missing utils module error
rubra example_pipeline.py --config example_config.py --style run
[achalk@merri examples]$ ../rubra/rubra.py example_pipeline.py --config example_config.py --style run
Traceback (most recent call last):
File "../rubra/rubra.py", line 86, in
main()
File "../rubra/rubra.py", line 35, in main
import(drop_py_suffix(args.pipeline))
File "example_pipeline.py", line 15, in
from rubra.utils import (runStageCheck)
ImportError: No module named utils
copying the example_pipeline.p, example_config.py and examples/test to rubra directory fixes this
But there is an error in the pipeline.
[achalk@merri rubra]$ rubra/rubra.py example_pipeline.py --config example_config.py --style run
Traceback (most recent call last):
File "rubra/rubra.py", line 86, in
main()
File "rubra/rubra.py", line 66, in main
gnu_make_maximal_rebuild_mode=rebuildMode)
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 2680, in pipeline_run
ruffus.ruffus_exceptions.RethrownJobError:
Exceptions running jobs for
'def example_pipeline.countLines(...):'
Original exceptions:
Exception #1
exceptions.AttributeError('NoneType' object has no attribute 'stages'):
for example_pipeline.countLines.Job = [test/data2.txt -> [test/data2.count, test/data2.count.Success]]
Traceback (most recent call last):
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
return_value = job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 447, in job_wrapper_io_files
ret_val = user_defined_work_func(*param)
File "example_pipeline.py", line 25, in countLines
runStageCheck('countLines', flagFile, file, output)
File "rubra/utils.py", line 132, in runStageCheck
status = runStage(stage, *args)
File "rubra/utils.py", line 143, in runStage
command = getCommand(stage, pipeline_options)
File "rubra/utils.py", line 175, in getCommand
commandStr = getStageOptions(options, name, 'command')
File "rubra/utils.py", line 104, in getStageOptions
return options.stages[stage][optionName]
AttributeError: 'NoneType' object has no attribute 'stages'
Exception #2
exceptions.AttributeError('NoneType' object has no attribute 'stages'):
for example_pipeline.countLines.Job = [test/data1.txt -> [test/data1.count, test/data1.count.Success]]
Traceback (most recent call last):
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
return_value = job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
File "build/bdist.linux-x86_64/egg/ruffus/task.py", line 447, in job_wrapper_io_files
ret_val = user_defined_work_func(*param)
File "example_pipeline.py", line 25, in countLines
runStageCheck('countLines', flagFile, file, output)
File "rubra/utils.py", line 132, in runStageCheck
status = runStage(stage, *args)
File "rubra/utils.py", line 143, in runStage
command = getCommand(stage, pipeline_options)
File "rubra/utils.py", line 175, in getCommand
commandStr = getStageOptions(options, name, 'command')
File "rubra/utils.py", line 104, in getStageOptions
return options.stages[stage][optionName]
AttributeError: 'NoneType' object has no attribute 'stages'
This runs on merri currently, so likely to be an installation issue. We probably need to add better installation instructions.