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Using the latest git version of Toil (last commit: dbbd4ed) with a gridengine batch system the HelloWorld pipeline runs, but does not terminate:
```
> python HelloWorld.py --batchSystem gridEngine --…
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```
#!/usr/bin/env python2.7
'''
Author : Arjun Arkal Rao
Affiliation : UCSC BME, UCSC Genomics Institute
File : toy_code_for_unfulfilled_promise_error.py
'''
from __future__ import print_function
fro…
arkal updated
6 years ago
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I created a cluster with a single worker node using cgcloud:
```
$ cgcloud create-cluster toil -z us-west-2a -s 1 -t t2.medium
```
I logged in, cloned the common-workflow-language and cwltool reposi…
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The command and output:
mesosbox@ip-172-31-16-87:~$ python2.7 sort.py --fileToSort ./file_to_sort.txt --batchSystem=mesos --mesosMaster=mesos-master:5050 aws:us-west-2:my-jobstore
ip-172-31-16-87:…
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If the statically defined child of a job F (that should be encapsulated but isn't) is passed a return value that was obtained from a dynamically defined child of F, then and EOFError is thrown. @hanne…
arkal updated
6 years ago
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Command and Output:
Apples-Air:examples paulsanghera$ python2.7 sort.py --fileToSort ./file_to_sort.txt file:jobStore
Apples-Air 2017-06-15 12:34:26,917 MainThread INFO toil.lib.bioio: Root logger i…
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mesosbox@ip-172-31-16-87:~$ python2.7 toil-sort-example.py --batchSystem=mesos --mesosMaster=mesos-master:5050 aws:us-west-2:my-jobstore
ip-172-31-16-87: 2017-06-15 17:54:06,215 INFO: toil.lib.bio…
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PR #431 (to be merged soon) makes the failure simulation in sortTest (look for badWorker in worker.py) much more aggressive. It now randomly kills the worker process instead of raising an exception in…
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I'm putting files in the global file store in a child job, returning their IDs thouugh the promise mechanism into the follow-on job's arguments, and then the follow-on job is complaining that it can't…
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When attempting to run vg-toil map or call, gzip and cat produce broken pipe errors.
I ran something like this:
`toil-vg map ./toiltmp SMPL1 all.xg all.gcsa ./toilout --fastq SMPL1.fastq --config…