Hi list,

I got the following tool_dependencies.xml file failing:

<?xml version="1.0"?>
<tool_dependency>
   <package name="bedtools" version="2.17.0">
       <install version="1.0">
           <actions>
        <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
        <action type="shell_command">make clean</action>
        <action type="shell_command">make all</action>
        <action type="move_directory_files">
            <source_directory>bin</source_directory>
            <destination_directory>$INSTALL_DIR/bin</destination_directory>
        </action>
        <action type="set_environment">
           <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
        </action>
           </actions>
       </install>
       <readme>
GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools
       </readme>
   </package>
</tool_dependency>

The error given is:

#############################################
make clean
STDOUT

#############################################

#############################################
make clean
STDERR
make: *** No rule to make target clean'.  Stop.
#############################################

I basically just copied the example code from the Galaxy wiki for R:

<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
    <package name="R" version="2.15.1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R.
        </readme>
    </package>
</tool_dependency>

I have found no documentation to what the tag <action type="download_by_url"> does...
I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn’t..

Any advice on this or at least a link to the pertinent documentation??

Thanks a lot in advance...

Franco

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