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.
On Mon, Oct 26, 2015 at 4:16 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
The tools using Bioptyhon etc should declare a dependency, see e.g.
Use a repository_dependencies.xml file declaring this as a dependency,
<repositories description="Requires Biopython as a dependency.">
<repository name="package_biopython_1_66" owner="biopython"
Also, in your tool XML file(s) you must include:
That should then trigger Galaxy to source the relevant env.sh files
when the tool is run.
On Mon, Oct 26, 2015 at 4:06 PM, Tony Schreiner
> 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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