Error adding new table to tool_data_table

Question: Error adding new table to tool_data_table_conf.xml

7 months ago by

gkuffel22 • 170

United States

gkuffel22 • 170 wrote:

Hi friends,

I am trying to add a genome to hisat2 and all is going well except when I try to add the new table info to the bottom of tool_data_table_conf.xml and then I restart the Galaxy server I get the following error:

Error parsing file ./config/tool_data_table_conf.xml
ParseError: junk after document element: line 104, column 0

Any ideas?

admin data install managers galaxy • 230 views

ADD COMMENT • link •

modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by gkuffel22 • 170

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This error probably means there is a formatting problem. Check for extra spaces, extra blank lines, and overall format. You can also compare the formatting against the sample from the distribution:

https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf.xml.sample

Using Data Managers to install genomes/indexes is an easier route. In your prior question (https://biostar.usegalaxy.org/p/27713/), I linked to another post that describes how to use these. In short, the genome should be installed first, then downstream indexes can be created.

Ephemeris could also be used. One of the utility package functions bundles together data install protocols/tools to make the processing much less tedious versus running individual data managers independently.

Attempting to do the admin data installs manually is error-prone and not recommended. Avoid doing this if at all possible. HISAT2's data manager is here in the ToolShed https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_hisat2_index_builder/d210e1f185bd. Others can be found under the Category "Data managers".

Thanks! Jen, Galaxy team

ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Yes, your link you provided in my previous post was extremely helpful and I am installing hisat indices using the Data Manager as we speak! I just wanted to have a thorough knowledge of how to do this manually as well. I also suspected a format issue but I don't know how that could be as I copied the table directly from tool_data_table_conf.xml.sample in the hisat2 directory and pasted directly into the tool_data_table_conf.xml file located in galaxy/config.

ADD REPLY • link written 7 months ago by gkuffel22 • 170

Ok, good that you are using Data managers. As for the formatting problems, even a space instead of a tab can cause problems (or the reverse!). I've done all of this manually too, as all indexes used to be created manually before DMs were developed, and little gotchas with formatting were always a hassle to find and fix. There is no automatic solution - you'll need to review the content carefully. Start with the whitespaces - those were the most common places I found formatting problems. Paths are another place to check for problems. Copy and paste works differently depending on the text editor used and can introduce small problems (again, usually whitespace problems).

For the details about config files with links to admins docs, you might also want to review here: https://docs.galaxyproject.org/en/master/admin/config.html

Hope this works out!

ADD REPLY • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Similar posts • Search »