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Question: Sam To Bam tool hangs in Cloning stage, though other tools, including Pilon, could be installed
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gravatar for msprindzhuk
20 months ago by
msprindzhuk • 50
msprindzhuk • 50 wrote:

Sam To Bam tool hangs in Cloning stage, though other tools, including Pilon, could be installed. How to fix that? Does anybody have experience with Sam 2 bamm tool installation problems? Is there any other tool or module for SAM to BAM conversion?
sam2bam samtools • 610 views
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modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by msprindzhuk • 50
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gravatar for Jennifer Hillman Jackson
20 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool suite installs without problems on a default 17.01 instance. Try uninstalling then reinstalling the tool.

If dependency/installation problems continue, please review the help here to ensure that managed dependencies are used: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html

Thanks! Jen, Galaxy team
ADD COMMENT • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k

Root problem likely related to your prior question: Conda problem during tool installation https://biostar.usegalaxy.org/p/22159/

We should follow up in one thread only, get Conda installed and used correctly, then troubleshoot more from there as needed.

ADD REPLY • link written 20 months ago by Jennifer Hillman Jackson ♦ 25k
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