Question: Need help with "Get Pathways" tool
gravatar for andr.agostinelli
3.9 years ago by
United Kingdom
andr.agostinelli0 wrote:


 i am trying to get the KEGG AND GO pathways fro a given ensemble of transcripts with no success and  I cannot figure out the nature of the error as my input file has been uploaded under the tabular format.  I compare this set with the last Human catalogue (2013). 




this is my stderr :


Traceback (most recent call last):
  File "/galaxy/main/shed_tools/", line 77, in <module>
  File "/galaxy/main/shed_tools/", line 43, in main
    crDB=[x.split() for x in open(loc_file).read().splitlines() if x.split()[0]==species][0]
IndexError: list index out of range



Tool name: Get Pathways
Tool version: 1.0.0
Tool ID:
ToolShed URL:


software error get-pathways • 1.0k views
ADD COMMENTlink modified 21 months ago by pabrennan0 • written 3.9 years ago by andr.agostinelli0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The immediate issue is that the tool is expecting a two-column input dataset. In your case, the build name is missing. Here is the help quote from the "Get Pathways" tool form:

Dataset formats

The input and output datasets are in tabular format. The input dataset must have a column with an ENSEMBL transcript ID and have the database/build set. Even though positions are not needed the correct database/build must be given to look up the pathways. The output dataset will have added columns for the pathway.

There is also a content issue, as these are gene identifiers, not transcript identifiers. For transcripts associated with this gene, I just searched at Ensembl, here is the page:;g=ENSG00000124731;r=6:41267926-41286719;t=ENST00000591620;redirect=no

Hopefully by making the necessary input corrections, things will work out, but please let us know if not. Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
gravatar for pabrennan
21 months ago by
pabrennan0 wrote:


My "Get Pathways" tool does not work as well. I get the same error message as the top guy, but I have mouse Ensembl transcripts, and I set the database/build to "Mouse Dec. 2011 (mm10)". My input is tabular with 16 columns and I have one column with the Ensembl transcript IDs. Is there anything else I can try to get the KEGG pathways?

Thanks, Paul

ADD COMMENTlink written 21 months ago by pabrennan0

Hi Paul, This is an older tool with no plans for an update. The list of genomes that will work (using the cached legacy reference data) are hg19, canFam2, and bosTau4. Unfortunately, data from mouse are not accepted. Other tools access KEGG pathways (for example, GEMINI), yet this may not meet your use case. A stand-alone tool for just this function (any list of Ensembl IDs -> KEGG pathway) does not exist yet. Jen, Galaxy team

ADD REPLYlink written 21 months ago by Jennifer Hillman Jackson25k
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