where to find cutadapt tool version / where to find the lastest tool

Question: where to find cutadapt tool version / where to find the lastest tool

9 months ago by

New York

18Kbeyond • 20 wrote:

Hi. When I searched for "cutadapt" here https://toolshed.g2.bx.psu.edu/ I see one result that "Installable Revision" is 2015-05-26. There are 3 results but the other two seem wrong - their "type" is "Tool dependency definition" and their revision dates are older.

The problem is, https://cutadapt.readthedocs.io/en/stable/ gives a list of versions and dates, and v1.8 is 2015-03-14 (while v1.15 is 2017-11-23).

Does it mean the cutadapt tool from Galaxy is v1.8 , not the latest one v1.15? If I am not looking at the latest one, where can I find the right one?

cutadapt trim-galore trim version trimmomatic • 449 views

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modified 9 months ago by Jennifer Hillman Jackson ♦ 25k • written 9 months ago by 18Kbeyond • 20

9 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool Cutadapt has not had the wrapper or underlying source updated for a few years as you have noticed. Try Trimmomatic instead - it performs the same function (CROP) plus more.

Please see this Galaxy tutorial for one example of usage:

https://galaxyproject.org/tutorials/ngs/#trimming-reads

You can, of course, modify the parameters for your own data. Options on the Galaxy tool form are the same as Trimmomatic's line-command, so the same tool manual applies to both concerning functions.

http://www.usadellab.org/cms/?page=trimmomatic

Thanks! Jen, Galaxy team

ADD COMMENT • link written 9 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you for the advice. For now I would like to stick to the same tool (Cutadapt).

The reason I asked for Galaxy's Cutadapt version is because I need to use Cutadapt before some downstream analysis --- I am trying to run Galaxy version as well as command line version, and comparing the results to make sure they are the same, so that I have confidence the xml scripts I wrote for downstream analysis are correct.

I see this post https://biostar.usegalaxy.org/p/318/ that we can download Galaxy tool to run in command line. Is there a link to show more detailed steps how I can do that?

ADD REPLY • link written 9 months ago by 18Kbeyond • 20

You'll need to set up your own Galaxy server, install this tool, then use the API.

I am not sure if the tool will even work in the most recent releases since the community author of the Galaxy wrapper has not updated it to reflect recent changes. But you can test that. If problematic, the author can be reached through the ToolShed (log in to the ToolShed, go to the tool, and a contact option is under the top right menu "Repository Actions").

That said, this tool wrapper might not be a target for updates from this author. If you want to help to update it (if needed) you could offer to do that at the linked development repository for the tool. Trim Galore! incorporates Cutadapt, which places the original Cutadapt tool in a deprecated state.

ADD REPLY • link modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson ♦ 25k

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