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Question: What Galaxy tools can convert SAM format to the BAM except SAM2BAM which can`t be installed on our instance?
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gravatar for msprindzhuk
20 months ago by
msprindzhuk • 50
msprindzhuk • 50 wrote:

What Galaxy tools can convert SAM format to the BAM except SAM2BAM which can`t be installed on our instance?
installation sam2bam cloud samtools • 510 views
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modified 20 months ago by Jennifer Hillman Jackson ♦ 25k • written 20 months ago by msprindzhuk • 50
1

SAM2BAM is samtools, so the question becomes why that can't be installed on your instance.

ADD REPLY • link written 20 months ago by Devon Ryan • 1.9k
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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,

Samtools is needed for other basic functions, such as uploading a BAM dataset to Galaxy. So you'll want to get this installed.

So, Devon is correct - fixing the Samtools installation is the root of the problem. We can follow up in your prior question if that is still a problem: https://biostar.usegalaxy.org/p/22161

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