Question: Cannot get scripts to show in Galaxy
gravatar for CMonger
2.8 years ago by
CMonger0 wrote:

Hi all,

I've been attempting to create and integrate a script into Galaxy using instructions in various tutorials and the official wiki but have yet to successfully do so.

I've placed the python script and an xml wrapper in /pathtogalaxy/tools/myTools/ and updated the config/tool_conf.xml file with the following:

  <section id="my_tools" name="My Tools">
    <tool file="my_tools/xy_plot.xml" />
    <tool file="my_tools/merge_htseq.xml" />

However the tools are not showing in the bar when I run the galaxy server and the automatically generated integrated_tool_panel.xml for this section does not appear to be showing the tools.

    <section id="my_tools" name="My Tools" version="">


The galaxy.ini also seems to be correctly configured as far as I can tell:

tool_path = /mnt/work/galaxy/galaxy/tools

tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml


Does anybody have any advice on what I'm doing incorrectly?

Thanks in advance,






software error galaxy • 959 views
ADD COMMENTlink modified 2.8 years ago by Martin Čech ♦♦ 4.3k • written 2.8 years ago by CMonger0

Can you show us contents of your xml files e.g. through the service?

ADD REPLYlink written 2.8 years ago by Martin Čech ♦♦ 4.3k

My apologies, just realized my xml was invalid. Fixed the syntax error and its now showing up. Thanks for pointing me to the cause of the problem!

ADD REPLYlink written 2.8 years ago by CMonger0
gravatar for Martin Čech
2.8 years ago by
Martin Čech ♦♦ 4.3k
United States
Martin Čech ♦♦ 4.3k wrote:

This is just to formalize that the problem is solved.

The reason for the tools not showing up was invalid tool syntax. The specification of syntax is here: and a tool that can lint/validate your tool syntax (and provide other help with writing Galaxy tools) is here:

ADD COMMENTlink written 2.8 years ago by Martin Čech ♦♦ 4.3k
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