Question: install all tools from repositories
gravatar for Mic
3.3 years ago by
Mic70 wrote:


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/ --api YOUR_API_KEY -l http://localhost:8080 --url -o bgruening --name chemicaltoolbox --tool-deps --repository-deps --panel-section-name ChemicalToolBoX

Thank you in advance. mic


toolshed repositories galaxy • 967 views
ADD COMMENTlink modified 3.3 years ago by Jennifer Hillman Jackson25k • written 3.3 years ago by Mic70

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

ADD REPLYlink written 3.3 years ago by Bjoern Gruening5.1k
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k


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 REPLYlink written 8 months ago by chenzhuod30

Most any tool can be wrapped and used within Galaxy. Planemo is strongly recommended for tool development projects:

Going forward, please post any new questions in a new thread. You might also consider the mailing list, as this reaches more developers.

ADD REPLYlink written 8 months ago by Jennifer Hillman Jackson25k
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