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Question: install all tools from repositories
0
gravatar for Mic
3.3 years ago by
Mic • 70
Australia
Mic • 70 wrote:

Hello,

How is it possible to install all tools from e.g. SAM Repositories from the toolshed? I found also  the below command which shows how to install the ChemicalToolBox, but I am not quite sure how to do is for e.g. SAM Repositories either from Galaxy or this command:

     python ./scripts/api/install_tool_shed_repositories.py --api YOUR_API_KEY -l http://localhost:8080 --url http://toolshed.g2.bx.psu.edu/ -o bgruening --name chemicaltoolbox --tool-deps --repository-deps --panel-section-name ChemicalToolBoX

Thank you in advance. mic

 
toolshed repositories galaxy • 967 views
ADD COMMENT • link •
modified 3.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.3 years ago by Mic • 70

Hi, what are SAM repositories? Can you provide us with a link?

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If you install the Samtools repository from the Tool Shed through the Admin interface tools, and leave the checkbox to install dependencies checked, you will get all of the tools. Also consider installing Picard since these two work together and have some overlapping dependencies. Picard also has basic useful tools that you will almost certainly want on your local.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

hello,

I want to install a software not exsit in Tool Shed. The software is a custom software, such as "fqtrim". can you guide me?

Best Siyuan Chen

ADD REPLY • link written 8 months ago by chenzhuod • 30

Most any tool can be wrapped and used within Galaxy. Planemo is strongly recommended for tool development projects: https://galaxyproject.org/tools/

Going forward, please post any new questions in a new thread. You might also consider the galaxy-dev@lists.galaxyproject.org mailing list, as this reaches more developers. https://galaxyproject.org/mailing-lists/

ADD REPLY • link written 8 months ago by Jennifer Hillman Jackson ♦ 25k
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