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Question: cutadapt custom file
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gravatar for zsmith
21 months ago by
zsmith • 10
United States
zsmith • 10 wrote:

Hello,

I'm working on a cloud instance of galaxy and we have installed cutadapt from the tool shed. I would like to be able to add a couple of tab delimited files with list of adaptors to the drop down selection. How do I go about editing the cutadapt_adaptor.txt.sample file or adding my own files to the repository?

cutadapt • 526 views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 21 months ago by zsmith • 10
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Instructions are listed in the README in the Tool Shed. In short, edit the sample file using the existing contents as an example. Any text editor would be appropriate (vim for example).

I am not sure if the server needs to be restarted after, but that easy to test out when you do the edits. If you have problems after that, or want to suggest updates to the core repo, contacting the tool author via the tool shed about them - or better - through the development repository (also linked from the tool shed) is the way forward.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen,

Thank you for the speedy response. I wouldn't call myself a programmer by any stretch of the imagination. How do I go about accessing the cloud instance through unix? Is this possible to do through the web interface?

ADD REPLY • link written 21 months ago by zsmith • 10

Hi Jen,

I've made the modifications to the cutadapt_adapters.txt file and restarted the cloud, but all I keep getting is an uncaught exception in exposed API method error and the tool failed to load. Can you offer any suggestions?

ADD REPLY • link written 21 months ago by zsmith • 10
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