Cufflinks Failure Error - Solution: use version 2.2.1.2 or later

Traceback (most recent call last): File "/jetstream/scratch0/main/jobs/19882713/tool_files/cufflinks_wrapper.py", line 9, in <module> from galaxy.datatypes.util.gff_util import parse_gff_attributes, gff_attributes_to_str File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/util/gff_util.py", line 6, in <module> from bx.intervals.io import GenomicInterval, GenomicIntervalReader, MissingFieldError, NiceReaderWrapper, ParseError ImportError: No module named bx.intervals.io

5 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This is a brand new dependency issue (today) and we will be correcting it. Please follow progress here: https://github.com/galaxyproject/usegalaxy-playbook/issues/146

Meanwhile, you might want to consider using the updated tools/workflows for RNA-seq covered in the Galaxy tutorials (and avoid this tool): https://galaxyproject.org/learn/

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

The problem is now fixed. Be sure to use the latest Cufflinks tool version (was just installed). Thanks!

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thanks for your help. I've created new jobs with the updated cufflinks - some went through and finished alright but others crashed and gave this error, do you think it's another bug?

thanks! Val

  File "/jetstream/scratch0/main/jobs/19888009/tool_files/cufflinks_wrapper.py", line 169
    print cmd
            ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(cmd)?

ADD REPLY • link written 5 months ago by VY • 120

First, make sure that you are using the latest version of Cufflinks.

Next, try a rerun, or better, switch to using Stringtie. That tool and others are covered in the Galaxy tutorial's link I sent.

Thanks!

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

I was unable to reproduce your problem (with any of the Cufflinks tool versions). You may be using a specific parameter that is buggy.

If you have time, please send in a bug report from the failed job and leave the inputs/outputs undeleted. Include a link to this Biostars thread for reference/link the two.

Even though Stringtie is an alternative tool, if there is a clear problem with this tool it would be good to characterize it.

How to send in the bug report: https://galaxyproject.org/issues/#usage-problem-reporting

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I was unable to reproduce it either. I rerun cufflinks on the same files with the same parameters a second time and it went through fine so must have been a temporary glitch somewhere. Sorry.

ADD REPLY • link written 5 months ago by VY • 120

No problem, glad the rerun worked out. Your job may have been executing during the update (best guess!). Thanks!

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

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