Question: Is galaxy create the binaries at the time of installing any tool from galaxy tool shed?
gravatar for Shirish
4.5 years ago by
Shirish20 wrote:

Hi all,

I upload my tool on galaxy

 Can anyone tell me, when we install it from galaxy tool shed to our local system at that time, is galaxy download the binaries of that particular tool on local system or it take it from url when we run that tool?




binaries toolshed galaxy • 1.3k views
ADD COMMENTlink modified 4.5 years ago by Martin Čech ♦♦ 4.9k • written 4.5 years ago by Shirish20
gravatar for fubar
4.5 years ago by
fubar1.1k wrote:

Thank you for contributing to Galaxy!

If a repository tool_dependencies.xml includes self installing packages as dependencies (such as package_bwa in the devteam bwa wrapper), they will be installed. Then, the local (eg bwa) binary is executed every time a user runs the tool locally. 

So, as I understand your question, yes.


ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by fubar1.1k

Hii Ross

Thanks for your reply, but in my tool I upload a tool_dependencies.xml file in repository with type tool dependency 

but it not install the binary anywhere in the local galaxy system,

This is tool_dependencies.xml file :

<?xml version="1.0"?>
    <package name="softesearch" version="0.6">
        <install version="1.0">
                 <action type="download_by_url">
        <action type="shell_command">perl ./ --prefix=$PWD</action>
                <action type="shell_command">export PERL5LIB=$PERL5LIB:$PWD:$PWD/lib</action>
        <action type="shell_command">perl script/</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>


So could you please tell me, is it correct code in XML file or not

and please tell me solution on this...

Thank You



ADD REPLYlink written 4.5 years ago by Shirish20

One approach might be to read the suggestions already made in response to one of your related posts at Error when install tool from galaxy tool shed .

If you "follow" your own questions you should be notified of updates automatically.

Please move all further discussion of your tool problems to your earlier question.

ADD REPLYlink modified 4.5 years ago • written 4.5 years ago by fubar1.1k
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