search paths for custom tools
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
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.schreiner@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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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.cock@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.schreiner@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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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