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getmlst tool on Galaxy #221

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JayanthiGangiredla opened this issue May 26, 2022 · 2 comments
Open

getmlst tool on Galaxy #221

JayanthiGangiredla opened this issue May 26, 2022 · 2 comments

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@JayanthiGangiredla
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Hi all,

We would like to request you to update getmlst tool on galaxy repo https://toolshed.g2.bx.psu.edu/repository?repository_id=5634a03143d6f21d.

Problem is the tool outputs the profile sequences but it doesn't give an output on MLST definitions for any species. Fixing the tool would be very useful for workflow development of MLST analysis.

Thanks,
Jayanthi Gangiredla
@apetkau apetkau mentioned this issue May 26, 2022
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@apetkau
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apetkau commented Jun 1, 2022

Thanks for reporting the issue. Since getmlst is mainly a Galaxy wrapper around getmlst.py from the srst2, do you know if it is all working with this tool outside of Galaxy? I did see this recent issue posted katholt/srst2#138, but I'm not sure if it's related.

I don't really have time right now to look into this, but at some point we may need to look into updating the getmlst and srst2 Galaxy tools.

@JayanthiGangiredla
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Thank you for your response.

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@apetkau @JayanthiGangiredla