While copying that from the Biopython Galaxy package README file, I
wondered if I had the wrong filename -  repository_dependencies.xml
should be tool_dependencies.xml which I'll fix now.

e.g.

https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans

Peter

On Mon, Oct 26, 2015 at 4:16 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> The tools using Bioptyhon etc should declare a dependency, see e.g.
>
> https://github.com/biopython/galaxy_packages
>
> Use a repository_dependencies.xml file declaring this as a dependency,
>
> <?xml version="1.0"?>
> <repositories description="Requires Biopython as a dependency.">
>   <repository name="package_biopython_1_66" owner="biopython" />
> </repositories>
>
> Also, in your tool XML file(s) you must include:
>
> <requirements>
>   <requirement type="package" version="1.66">biopython</requirement>
> </requirements>
>
> That should then trigger Galaxy to source the relevant env.sh files
> when the tool is run.
>
> Peter
>
> On Mon, Oct 26, 2015 at 4:06 PM, Tony Schreiner
> <anthony.schrei...@bc.edu> wrote:
>> Beginner question, I apologize.
>>
>> I recently set up a galaxy server for the first time.
>>
>> The users of this server are installing custom tools of their own creation.
>> Some of these tools use binaries from fastx_toolkit, and python libs from
>> biopython. Both of these have been added from tool_shed.
>>
>> I have not understood yet, how to set the search path for these dependencies
>> in the custom tools.  I see the env.sh files in the tool_shed directories,
>> but am now wondering if there is way to specify in the custom tools' xml
>> files how to invoke the needed env.sh. Or what is the more proper way to do
>> do this.
>>
>> Tony Schreiner
>> Boston College
>>
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