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Ruffus tasks involving file paths > 85 characters are failing when running 'make'.
It seems that either ruffus's pipeline_printout() or StringIO.getValue() splits lines > 85 characters, meaning the s…
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Documentation is for 2.3b1 but when I go to download link on pypi.python.org or
code.google.com, only 2.2 shows. Is Ruffus defunct?
```
Original issue reported on code.google.com by `erxnme...…
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Verbosity levels for pipeline_printout and pipeline_run do not seem to be
synchronised. It is not clear what exactly increasing verbosity does at each
level. What is more, different things seem …
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I believe the example code in the tutorial was included as images:
http://www.ruffus.org.uk/tutorials/simple_tutorial/step1_follows.html
Would it be possible to include the example code as text, …
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Hi,
Recently I tried to assemble several BAC clones one by one. All clones were sequenced by Hiseq2000.
At first, I mapped all reads to BAC and E. coli genome sequences and resultant bam files consis…
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In Python 3, process.communicate() returns bytes, not strings. Calling
stream.write(result_str) in ruffus.graph.graph_printout() causes an exception.
The solution is to open the output file with…
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Having the ruffus directory nested in the src/ subdirectory prevents "sudo
python setup.py develop" from working properly. Granted that's probably a
bigger issue with setuptools, but it does mak…
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The pipeline does not halt, and exceptions are not forwarded until the pipeline
has collected NNN jobs worth of exceptions where NNN = multiprocess.
Even if this behaviour is retained, the text …
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What steps will reproduce the problem?
1. cd doc
2. make html
What is the expected output? What do you see instead?
I expect to generate documentation on my machine. This works.
But then I get …
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split operations which produce many output jobs should be printed as such:
Task = split_animals
Job = [None
->cows.animal
->horses.animal]
instead of
Task = sp…