Cufflinks dependency problem error - Solution: use version 2.2.1.2 or later

Traceback (most recent call last): File "/jetstream/scratch0/main/jobs/20147175/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

4 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This problem has been corrected. Please try a rerun and make sure that you switch to using the new updated tool version: Galaxy Version 2.2.1.2

Also please consider using Stringtie instead along with the current RNA-seq tools described in the Galaxy tutorials:

https://galaxyproject.org/learn/

Cufflinks and the related tools from that tool suite are much older and it is strongly recommended to use the newer methods going forward.

Thanks for reporting the issue, Jen, Galaxy team

ADD COMMENT • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Dear Jennifer,

Thanks for your help. It works now, however, I have another question about the cufflinks. When I tried the cufflinks in Galaxy, the result showed the lowest gene expression is no more than 0.00005, but I had tried on cufflinks tool downloaded from their official sites, I found the result showed the lowest gene expression is less than 1e-100. I am confused about this phenomenon, any suggestion?

Thanks

ADD REPLY • link written 4 months ago by garentguuu • 10

The difference is most likely due to using different parameters between the two runs.

Many wrapped tools, including Cufflinks, have default parameters plus advanced parameters. These can all be adjusted on the tool forms. Galaxy provides a web interface but jobs are still submitted line-command for execution. The 3rd party tool's computational core is not modified.

Tool version, input/reference data, OS, etc differences could also be a factor, but first, compare parameters.

ADD REPLY • link written 4 months ago by Jennifer Hillman Jackson ♦ 25k

Dear Jennifer,

Thanks for you reply. As your advise, I have checked all parameters with Galaxy, it is still not the same. My line-command result still has very low value, also my cufflinks version is v2.2.1. I am curious about the 3rd party: "tool's computational core is not modified", how can I modify my cufflinks withe line-command?

Thanks very much!

ADD REPLY • link written 4 months ago by garentguuu • 10

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