Question: What Galaxy tools can convert SAM format to the BAM except SAM2BAM which can`t be installed on our instance?
0
gravatar for msprindzhuk
17 months ago by
msprindzhuk50
msprindzhuk50 wrote:

What Galaxy tools can convert SAM format to the BAM except SAM2BAM which can`t be installed on our instance?

ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson25k • written 17 months ago by msprindzhuk50
1

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

ADD REPLYlink written 17 months ago by Devon Ryan1.9k
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gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k 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 COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k
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