Need help with "Merge BAM Files" tool-large number of files to merge into one

Question: Need help with "Merge BAM Files" tool-large number of files to merge into one

3.8 years ago by

Germany

guyreeves • 10 wrote:

I want to merge at lot >40 of individual bam files into one.

Is there an easier way to do this than having to select each .bam file as an input?

In my work flows I use 'data collection lists' it would be great if there was a way to use the list to merge all files into one.

I can see that this has been thought of, see page 19and 20

https://www.e-biogenouest.org/resources/1202/download/Chilton.pdf

As far as I can tell this really useful idea has not yet been implemented. Is this correct?

Are there other tools by which I could lists .bam or sam files so I can take them into a genotype/SNP calling tool?

Thanks In advance

Guy

Tool name: Merge BAM Files
Tool version: 1.1.2
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.1.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/devteam/sam_merge

merge-bam-files galaxy • 1.5k views

ADD COMMENT • link •

modified 3.8 years ago by Guy Reeves • 1.0k • written 3.8 years ago by guyreeves • 10

That is great thanks.

ADD REPLY • link written 3.8 years ago by Guy Reeves • 1.0k

Hi, if you could accept Bjoern's answer (click on the checkmark next to the post below), that would be very nice and help others who have the same issue find the post. Thanks! Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

Hi I would be happy to do this but I have looked and looked but I can not see a check box. I have 'upvoted' but I guess this is not the same. Thanks Guy

ADD REPLY • link written 3.8 years ago by Guy Reeves • 1.0k

3.8 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

I updated the wrapper in this PR: https://github.com/galaxyproject/tools-devteam/pull/57

If we are lucky this get's merged and we can update the ToolShed.

Thanks,

Bjoern

ADD COMMENT • link written 3.8 years ago by Bjoern Gruening ♦ 5.1k

Thanks a lot Bjoern for looking into this , this will be so useful.

Does your message mean that this option will be available on the 'usegalaxy.org' user interface soon? Will it be available in workflows?

Thanks

Guy

ADD REPLY • link written 3.8 years ago by guyreeves • 10

Workflows yes. But I doubt that it will be available soon on usegalaxy.org. The Galaxy teams as a very strict testing policy afaik. So this can take some time. Martin or Jen are help you with this more than I can.

ADD REPLY • link written 3.8 years ago by Bjoern Gruening ♦ 5.1k

Thanks for your patience, I am very new to Galaxy. So to get to use your modification, I will need to instal a local version of Galaxy and then instal it from the toolshed?

Thanks Guy

ADD REPLY • link written 3.8 years ago by guyreeves • 10

Let's ask the usegalaxy.org admins. If you really need to install a Galaxy instance locally, we have a Docker container for you, which might help you in this.

https://github.com/bgruening/docker-galaxy-stable

ADD REPLY • link written 3.8 years ago by Bjoern Gruening ♦ 5.1k

I updated the devteam's repository on the Tool Shed with the latest updates from Bjoern. https://toolshed.g2.bx.psu.edu/view/devteam/sam_merge

The tool will probably be updated in the next update batch that will happen on usegalaxy.org during next month.

ADD REPLY • link written 3.8 years ago by Martin Čech ♦♦ 4.9k

That is great thanks

ADD REPLY • link written 3.8 years ago by Guy Reeves • 1.0k

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