Hello David,

I've just committed change set 7656:6aadac8026cb to the Galaxy central 
repository that provides the ability to do what you need here.  It would be 
great if you could try things out and let me know if you run into any problems. 

I've been working with nikhil-joshi's deseq_and_sam2counts repository in the 
main Galaxy tool shed because his tools require this new feature as well.  This 
example should provide you with the information you'll need to tweak your tool 
shed repository so that your tool dependencies are located where they get 
installed rather than attempting to move them to ${GALAXY_DATA_INDEX_DIR} or 
some other location.

Here is the tool_dependency.xml file entry for locating a directory referred to 
by an environment variable name R_SCRIPT_PATH.

<?xml version="1.0"?>
    <set_environment version="1.0">
        <environment_variable name="R_SCRIPT_PATH" 

The <set_enviroment> tag, is still supported inside <package> tag sets, but 
when defined at the xml root level, it will locate dependencies included in the 
installed tool shed repository.  Of course, the above tool_dependencies.xml 
file could of course also include entries for tool dependencies that are 
packages, For example:

<?xml version="1.0"?>
    <set_environment version="1.0">
        <environment_variable name="R_SCRIPT_PATH" 
    <package name="R" version="2.15.1">
        <install version="1.0">
                <action type="shell_command">./configure 
                <action type="shell_command">make</action>
                <action type="set_environment">
                    <environment_variable name="PATH" 
You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build 

These tool dependency definitions are handled as described in the following 
section of the tool shed wiki:


So in order for the dependencies to be handled when the repository is 
installed, they must be defined in at least one of the <requirement> tag sets 
in at least 1 tool config in the repository.  So, the <requirements> tag set in 
the deseq.xml tool config file will look something like this (there are more 
requirement tags defined here than in the tool_dependencies.xml fiel above, but 
you should get the idea).

        <requirement type="set_environment">R_SCRIPT_PATH</requirement>
        <requirement type="package" version="2.15.1">R</requirement>
        <requirement type="package" version="2.10">Bioconductor</requirement>
        <requirement type="package" version="1.8.3">DESeq</requirement>
        <requirement type="package" version="1.24.0">aroma.light</requirement>
        <requirement type="package" version="0.20-6">lattice</requirement>

The <command> tag set in the deseq.xml tool config is also slightly altered.  
Here is the way it looks before using this new approach:

<command interpreter="python">
         stderr_wrapper.py Rscript ${GALAXY_DATA_INDEX_DIR}/deseq.R $counts 
$column_types $comparison $top_table $diagnostic_html 
"$diagnostic_html.files_path" "$counts.name"

To use this new feature, the command string now uses the R_SCRIPT_PATH 
environment variable ( notice the required backslash to escape the $ )

<command interpreter="python">
    stderr_wrapper.py Rscript \$R_SCRIPT_PATH/deseq.R $counts $column_types 
$comparison $top_table $diagnostic_html "$diagnostic_html.files_path" 

When installed from the tool shed, a tool dependency object named R_SCRIPT_PATH 
will be created and associated with the installed repository.  The dependency 
will have a pointer to the env.sh file that is created to set the value of the 
R_SCRIPT_PATH environment variable.

Let me know if you bump into any issues in getting this working for your tools.


Greg Von Kuster

On Sep 12, 2012, at 1:00 PM, David Hoover wrote:

> Are there any environment variables that are honored by toolshed installed 
> tools?  I tried creating a tool that uses ${GALAXY_DATA_INDEX_DIR} or 
> $GALAXY_HOME, then uploaded it the test toolshed, then installed it 
> automatically.  Neither of these resolved to what I expected.  I don't want 
> to hard-code the path in the xml tool file, but rather have a default 
> location for other executables and jar files.  How should this best be done?
> David Hoover
> Helix Systems Staff
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