Question: How to test tool_dependencies.xml
gravatar for alexander.lenail
2.7 years ago by
alexander.lenail0 wrote:

I'm trying to make a tool on the tool shed, which has a dependency called chipsequtil. I've written a tool_dependencies.xml file which I think should properly install chipsequtil. But after I install the tool to my galaxy (using the tool shed) and try to run the tool, I get the following error: ImportError: No module named chipsequtil which is triggered partway through the actual script that I'm trying to run, when I try to import chipsequtil.

By following the steps in chipsequtil's readme, I'm capable of getting a functional chipsequtil version up and running locally.

Is there any way to test a tool_dependencies.xml file? I couldn't find one in planemo.

I've copied it here if there's an easy-to-spot error instead:

    <package name="chipsequtil" version="1.0">
        <install version="1.0">
                <action type="download_by_url"></action>
                <action type="shell_command">unzip -d chipsequtil</action>
                <action type="shell_command">cd chipsequtil</action>
                <action type="shell_command">cp org_settings.cfg src/chipsequtil/</action>
                <action type="shell_command">python install</action>
toolshed tools • 1.0k views
ADD COMMENTlink modified 2.7 years ago by Bjoern Gruening5.1k • written 2.7 years ago by alexander.lenail0
gravatar for Dave B.
2.7 years ago by
Dave B.410
United States
Dave B.410 wrote:


The fastest way to make this XML work is by adding the following after the install command in the last <action> tag: --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin, then creating a set_environment action tag as described at

The best-practices way is to create a dependency on a python repository in the toolshed, then using the setup_python_environment action type, as is done in

Naturally, you won't need all of the dependencies deeptools requires, so a little experimenting will be needed to find the minimum working set.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Dave B.410

Can you link me to an example of a similar use of the set_environment action tag? I'm not sure I quite understand what it is or how to use it, but if I see it used in practice somewhere, I may be able to piece together what exactly it's doing.

ADD REPLYlink written 2.7 years ago by alexander.lenail0

Yes, this link will highlight the set_environment actions in the xml I referenced above:

The first two are the important ones for any python package, letting the galaxy framework know how to find executables and python libraries. The rest are more relevant to packages that are used as dependencies by other packages.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by Dave B.410

Strangely, this still isn't working. My tool_dependencies.xml file looks like:

        <install version="1.0">
                <action type="download_by_url"></action>
                <action type="shell_command">cp org_settings.cfg src/chipsequtil/</action>
                <action type="shell_command">python install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>

When I go to galaxy_storage/galaxy-central/tool_deps/chipsequtil/1.0/alenail/chipsequtil/4f66143b385a I find what looks like a viable installation, but I'm still getting the same error. A file called reads:

PATH=/galaxy-central/tool_deps/chipsequtil/1.0/alenail/chipsequtil/4f66143b385a/bin:$PATH; export PATH
PYTHONPATH=/galaxy-central/tool_deps/chipsequtil/1.0/alenail/chipsequtil/4f66143b385a:$PYTHONPATH; export PYTHONPATH
CHIPSEQUTIL_ROOT_DIR=/galaxy-central/tool_deps/chipsequtil/1.0/alenail/chipsequtil/4f66143b385a; export CHIPSEQUTIL_ROOT_DIR

When I open python (this is on the vm) and try to import chipsequtil, it still fails (ImportError: No module named chipsequtil). This still works on my local machine.

ADD REPLYlink written 2.7 years ago by alexander.lenail0

Yes, the PYTHONPATH definition needs to be $INSTALL_DIR/lib/python

ADD REPLYlink written 2.7 years ago by Dave B.410
gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Just want to add that if you have a conda package available you also could use this as dependency.

ADD COMMENTlink written 2.7 years ago by Bjoern Gruening5.1k
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