Question: tool_dependencies.xml Not Working - Why?
gravatar for mltaylor211
3.3 years ago by
mltaylor2110 wrote:

I am working on writing a Galaxy tool that will run the genome assembly tool BUSCO. I have found that BUSCO has a few environment variables and path updates that need to be specified/exported before use. As such, I am trying to write a tool_dependencies.xml file to get this set up. It seems that what I have written so far has not been successful in exporting these environment variables.

Here is what I have written under the requirements tag in the XML file I wrote for my tool:

<tool id="g4" name="busco" version="0.0.2">
    <requirement type="package" version="3.0.1">BUSCO</requirement>
    <requirement type="set_environment">BUSCO_CONFIG_FILE</requirement>
    <requirement type="set_environment">AUGUSTUS_CONFIG_PATH</requirement>

Here is what I have written in my tool_dependencies.xml file:

<?xml version="1.0"?>
    <environment_variable action="set_to" name="BUSCO_CONFIG_FILE">/opt/galaxy/galaxy-app/tools/busco/busco/config/config.ini</environment_variable>
    <environment_variable action="set_to" name="AUGUSTUS_CONFIG_PATH">/opt/galaxy/galaxy-app/tools/busco/augustus/config/</environment_variable>
    <package name="BUSCO" version="3.0.1">
            <action type="set_environment">
                <environment_variable action="prepend_to" name="PATH">/opt/galaxy/galaxy-app/tools/busco/augustus/bin/</environment_variable>
                <environment_variable action="prepend_to" name="PATH">/opt/galaxy/galaxy-app/tools/busco/augustus/scripts/</environment_variable>

Any feedback or advice as to how I can improve my code would be greatly appreciated.

xml tool dependency assembly galaxy • 1.1k views
ADD COMMENTlink modified 3.2 years ago by martenson380 • written 3.3 years ago by mltaylor2110

You'll get a faster response to this on the galaxy site.

ADD REPLYlink written 3.3 years ago by Devon Ryan97k

Thank you, I will post the question there as well.

ADD REPLYlink written 3.3 years ago by mltaylor2110

Did you open this on the Galaxy Q&A site? Could you add the link here please.

ADD REPLYlink written 3.2 years ago by Peter5.8k
gravatar for martenson
3.2 years ago by
martenson380 wrote:

BUSCO seems to be available in the bioconda channel of the conda package manager. Thus you can use it already in Galaxy and all you need is the proper <requirement> tag in your Galaxy tool wrapper.

There shouldn't be a need to make a Tool Shed package recipe for it, unless you need to use it on an older Galaxy.

ADD COMMENTlink written 3.2 years ago by martenson380
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1698 users visited in the last hour