Hi Jorrit, 

Welcome.  It will be great to have your contributions to the toolshed.  

I think the main documentation for tool_dependencies.xml is here


Under “download_binary” you can see an indication of how to setup a tool to download a specific binary for a specific platform.

There is more info on this particular tag here


To be honest I’ve never used those tags myself.  The best thing would be to search around on the toolshed for recipes that work and take a look at the syntax they have used.  Note that just because a tool is on the toolshed it doesn’t mean that it is using correct toolshed syntax, or even that its installation would work properly.  The best place to look for examples would be the IUC tools 


And for proteomics specific stuff most of our tools have pretty good (working) toolshed xml


Oh .. and one final thing.  I highly recommend planemo for developing/testing tools for the toolshed if you are not using it already



On 8 Apr 2016, at 12:40 AM, Jorrit Boekel <jorrit.boekel@scilifelab.se> wrote:

Hi Galaxy-P,

I would like to package some tools for the toolshed and include them in the Galaxy-P github repo. The tools are:
- percolator and pout2mzid
- hardklor/kronik
- msstitch (aka my own tool)
And maybe some isobaric protein quant R script, and/or updates to MSGF+.

Anyway, I have poked around a little and have no problems creating and testing tools. However the toolshed syntax is a bit confusing. I understand I have to specify a package definition (tool_dependencies.xml) which installs the tool. And then the tool itself, which seems easy enough.

My questions about this:
- Is there any doc on the toolshed XML that defines how you install your binaries? I am planning to build from source, since percolator has binaries for different linuxes. (If it is not possible to specify which one of those to use.)
- what is in the admin-scripts directory? Static data?

Hoping to submit pull requests soon!


Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden

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