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Question: HISAT2 soft clipping
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gravatar for hermane
8 months ago by
hermane • 0
hermane • 0 wrote:

When using default options HISAT2 performs soft clipping. Under scoring options soft clipping is set to NO When scoring options is opened and executed is pressed an error is reported:

tool error An error occurred with this dataset: cannot find 'scoring_options'

When soft clipping is set from default NO to YES the same error is reported.

How can I run HISAT2 without soft clipping?
software error 2.1.0 usegalaxy.org hisat2 • 300 views
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modified 8 months ago by Jennifer Hillman Jackson ♦ 25k • written 8 months ago by hermane • 0
0
gravatar for Jennifer Hillman Jackson
8 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

I can reproduce the problem with the most current tool version at Galaxy Main https://usegalaxy.org: HISAT2 A fast and sensitive alignment program (Galaxy Version 2.1.0)

Some tests are still running to find out when this was introduced as a problem and if it is server-specific or not. Once completed, I'll comment on this ticket with details: https://github.com/galaxyproject/tools-iuc/issues/1792

Thanks for reporting the problem!

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

This has been confirmed to be a problem with the tool wrapper, see latest comments in the ticket.

Test jobs are still executing for the older tool versions - I'd like to be able to give you a workaround. The test history is linked in the ticket.

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