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Question: Need help with "SICER" tool
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gravatar for Law, Michael J.
4.4 years ago by
Law, Michael J. • 20
United States
Law, Michael J. • 20 wrote:

How can you add a genome to SICER in Galaxy?

 

 

Tool name: SICER
Tool version: 0.0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/sicer/peakcalling_sicer/0.0.1
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/sicer

 
add genome sicer • 1.8k views
ADD COMMENT • link •
modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by Law, Michael J. • 20
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

In the repository's 'sicer_wrapper.py' file, change this line:

VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ] 

The genome name should be an exact match for a dbkey in a local reference genome build set up on your local/cloud install. I believe that the 2bit file is the specific dependency.

Best, Jen, Galaxy team
ADD COMMENT • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

Thank you Jen for the reply. I am unsure about where to find the repository's "sicer_wrapper.py" file. Is there a path to this somewhere that is obvious and I am just missing it?

ADD REPLY • link written 4.4 years ago by Law, Michael J. • 20

It is on the top level of the hierarchy. If you go to the Tool Shed and just browse the repository, the upper right menu has an option to look at the tip files. These directories expand. 

Locally, these are generally installed into "tool-data". This wiki has the config options:
https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy

On a local Galaxy this would be likely here, perhaps nested in another subdirectory, if that is how you have it configured: ../galaxy/tool-data/<repo>

On a cloud Galaxy, native tools that come in the basic install are here:
/mnt/galaxy/galaxy-app/tool-data/<wrappers_not_bundled_into_repositories>
And Tool-shed tools are most likely here:
/mnt/galaxyTools/<repo>

The path may vary a bit, with <author>/<repo>/<content>

The Cloud updates frequently, so if I have an error in these paths, just look around the area a bit, you'll find the content. And someone from our team/community will likely post an update with what is most current.

Thanks! Jen, Galaxy team

ADD REPLY • link written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks again! I was just writing to you that I located the file, and am now working on editing it and moving it to my cloud instance of Galaxy. I will work on it and let you know how everything progresses.

I appreciate your help!

Mike

 

ADD REPLY • link written 4.4 years ago by Law, Michael J. • 20
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