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Question: Merging BAM files: bamtools not found
1
gravatar for skasowitz
2.9 years ago by
skasowitz • 70
skasowitz • 70 wrote:

I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned sequences from each lane into a single BAM file. When I attempt to use bamtools on usegalaxy.org I am receiving the following error:

Fatal error: Exit code 127 ()
/galaxy-repl/main/jobdir/011/351/11351255/galaxy_11351255.sh: line 42: bamtools: command not found

Is there a different way I should go about merging the data from different lanes? 
bamtools galaxy • 946 views
ADD COMMENT • link •
modified 17 months ago by cpreviti • 0 • written 2.9 years ago by skasowitz • 70
1

Hello,

We can confirm that there is an issue with all three tools in NGS: BamTools group at http://usegalaxy.org. Our team will review. Feedback/resolution may occur after the upcoming holiday.

Thanks for reporting the problem! Jen, Galaxy team

ADD REPLY • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k
2
gravatar for Martin Čech
2.9 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

This issue is now resolved, sorry for the trouble.
ADD COMMENT • link written 2.9 years ago by Martin Čech ♦♦ 4.9k
1

Thank you and Happy New Year!

ADD REPLY • link written 2.9 years ago by skasowitz • 70
0
gravatar for cpreviti
17 months ago by
cpreviti • 0
cpreviti • 0 wrote:

Dear Galaxy Team,

Could you tell me how this issue was resolved? I am having the same problems with BamTools in our local Galaxy instance, despite having installed the latest version (while running the latest Galaxy version).

Best regards, Christopher Previti
ADD COMMENT • link written 17 months ago by cpreviti • 0
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