Convert SAM to BAM without sorting

usegalaxy.eu support
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1

Dear Galaxy Admins,

I hope this message finds you well. I am currently working on a project that requires the use of the sam_to_bam tool, specifically version 2.1.1, from the following ToolShed repository:

bash

Copy code

toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1.1

I have searched for this tool version in the available tools on usegalaxy.eu, but it does not seem to be available. Since this particular version is critical for my analysis workflow, I kindly request that you install it on the usegalaxy.eu instance.

Please let me know if this is possible or if any further information is required. I appreciate your time and assistance in this matter.

Thank you very much for your support.

Best regards,
ASMA IVAZEH
asmaevazeh69@gmail.com

2

Welcome, @asma_ivazeh

This is the version we are using on the public UseGalaxy servers:

More about finding repositories

  1. You can search the ToolShed directly with keywords
  2. Or, you can check to see if it is hosted at a public Galaxy server: the server you like to work at, or one of the larger servers like UseGalaxy.org, UseGalaxy.eu, UseGalaxy.org.au
  3. Load up the tool form
  4. Click on the Options menu
  5. Select the option for See in Tool Shed

Screenshot

options-see-in-tool-shed

Hopefully this helps! I wasn’t sure if you have a question about sorting, so you can ask follow up questions. I can let you know that when you create the BAM, the default sort order is a “coordinate sort” and you’ll see the appropriate header flag for that at the top of the BAM. You can modify this as needed but most tools will expect that sort order. :slight_smile: