Question: How to install "NGS: Indel Analysis" tools
gravatar for Mic
3.4 years ago by
Mic70 wrote:

How is it possible to install `NGS: Indel Analysis` tools

on the local Galaxy.

Thank you in advance.

galaxy • 1.2k views
ADD COMMENTlink modified 2.5 years ago by jhardy0 • written 3.4 years ago by Mic70
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Start by making sure that all of the instructions at are followed (the first wiki, and Production server as needed). More help can be found under:

To install any tool, become an administrator on your instance, then use the top "Admin" tab. Under the section "Tool sheds -> Search and browse tool sheds" access the Main Tool Shed to install tools. Installed tools can be reviewed under "Server -> Manage installed tool shed repositories". To learn which exact repository is a match for a tool on an existing Galaxy instance, bring that tool up in the server's UI, and use the upper right corner pull down menu. A link to the Tool Shed will be present.

Best, Jen, Galaxy team



ADD COMMENTlink written 3.4 years ago by Jennifer Hillman Jackson25k

Hello, Thank you for response. I created an admin account and was able to install tools such BWA, but I am not able to find the above  `Indel Analysis tools` in the Tool Shed. Could you please tell me what is the exact name of these tools so I would be able to find them in the tool shed?

ADD REPLYlink written 3.4 years ago by Mic70

These tools were hosted at the GVL Galaxy server, but do not appear to be there any more. I am not sure which tools these are in the Main tool shed (, if they were ever there (could be hosted in another Tool Shed or not in one). This is a distinct server from Galaxy Main (

You could try contacting the GVL administrators and asking them about the tools. Thanks, Jen

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson25k
gravatar for jhardy
2.5 years ago by
United States
jhardy0 wrote:

Hello! Did you ever get a solution? I am having the same exact problem. All of the NGS tools are available on the main galaxy page but not in the tool shed. I cannot find them in the experimental tool shed either (e.g. convert solid output to fastq).

ADD COMMENTlink written 2.5 years ago by jhardy0

Tools that one can find on Galaxy Main are either part of the distribution or in the Tool Shed (

If you find a tool at that you wish to install into a local or cloud Galaxy, click on the tool name to bring the form up in the middle panel then from the Options menu select "See in Tool Shed":

enter image description here

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson25k
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