Hi Everyone,
Recently, I tried to use GATK - Depth of Coverage tool with my own .bam file on
Galaxy for the first time. However it gave following error for each output.
(see screenshot)
> Depth of Coverage on data 4 and data 1 (output cumulative coverage
> proportions sample)
> error:
> An error occurred with this dataset: /bin/sh: 1: samtools: not found
> Traceback (most recent call last): File
> "/home/can/galaxy-dist/tools/gatk/gatk_wrapper.py", line 126, in if
> __name__=="__main__": __main__() File
> "/home/can/galaxy-dist/tools/gatk/gatk_wrapper.py", line 9
I searched the mailing list, but I couldn't find similar problem that posted
before.
How can I solve it? Should I install GATK seperately on Galaxy? or anything
else?
Can Holyavkin
PhD Student
Istanbul Technical University
Molecular Biology and Genetics Dept.
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