Question: How To Add Tools Not Existed In Tool Shed To Local Galaxy
2
gravatar for camelbbs
5.7 years ago by
camelbbs660
China
camelbbs660 wrote:

I read the official instructions in galaxy about this question but still can't get aware of it. Hope someone can help. https://wiki.galaxyproject.org/Admin/Config/ToolDependencies

I got the galaxy-dist folder on my home directory. And run: sh run.sh Then can login to local galaxy by type http://localhost:8080 in browser.

Since the base version of local galaxy doesn't contain many important tools: like bedtools, bedops, samtools, etc. (I can't find them in Tool Shed). So I want to install some softwares manually.

I downloaded the tools I need to my local folder: ~/tools/, and then make them. Then I can run them from command line (Mac OS). But I don't understand how to add them to galaxy panel. I have set this tools folder to the galaxy tool_dependency_dir=~/tools/.

And what else I need to setup. It seems I need to write a XML file and a LOC file. And where I can add the "requirement" tag in galaxy. I can't find it.

Thanks very much

local galaxy • 5.5k views
ADD COMMENTlink modified 5.7 years ago by Ido Tamir5.0k • written 5.7 years ago by camelbbs660
2

https://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial

ADD REPLYlink written 5.7 years ago by Dr. Mabuse47k

Seems I need to write XML for each tool. Is there some existed XML file for these tools?

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by camelbbs660

That is correct. The most simple way is one tool = one XML tool definition (sometimes called 'wrapper'). If you go to the tool page in the Tool Shed (e.g. http://toolshed.g2.bx.psu.edu/repos/aaronquinlan/bedtools ) and click on the link next to 'hg clone' and then hit 'browse' you can directly browse the repository with the XML files to learn from them. There is also tutorial for creating a Histogram-like tool at https://wiki.galaxyproject.org/Admin/Tools/AddingTools and even example XML file to get you started at https://wiki.galaxyproject.org/Admin/Tools/ExampleXMLFile

ADD REPLYlink modified 5.7 years ago • written 5.7 years ago by martenson380

Thanks emulatorer. For another question I don't want to open a new issue: how to merge two different galaxy repositories. For example: galaxy-dist and galaxy-central. Can I just download them separately and overwrite the folder and files?

ADD REPLYlink written 5.7 years ago by camelbbs660

Why do you want to do that? Doesn't sound like a good idea to me.

ADD REPLYlink written 5.7 years ago by martenson380

OK. Thanks emulatorer, I may don't understand how the repositories run. I just think I can get more tools if I merge them in one folder.

ADD REPLYlink written 5.7 years ago by camelbbs660

Galaxy Tool is not just a folder, you cannot do that. The implications of such action are numerous and unpredictable. All tools that are or were at some time in Galaxy Main usegalaxy.org) are present in the Tool Shed.

ADD REPLYlink written 5.7 years ago by martenson380

As @Ido Tamir answered some of these tools are available in the Tool Shed and because its search is not very reliable yet you have to poke around a little (e.g. search for a tool id as 'bedtools' would give you a result) - we know about it and are working to improve it. A good start for wrapping a custom tool into Galaxy would be the Admin Tool hub page on the wiki: https://wiki.galaxyproject.org/Admin/Tools and also the tutorial that @Michael Dondrup linked.

ADD REPLYlink written 5.7 years ago by martenson380
3
gravatar for Ido Tamir
5.7 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:
ADD COMMENTlink written 5.7 years ago by Ido Tamir5.0k
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