I am using https://hub.docker.com/r/bgruening/galaxy-stable
I aded path to the samtools because I was getting error after installing samtools from toolshed.
Thank you, Deepak
On Aug 14, 2017, at 12:10, Peter Cock <p.j.a.cock@googlemail.commailto:p.j.a.cock@googlemail.com> wrote:
Galaxy itself uses samtools for many operations, which is different from when samtools is called as a dependency of a tool run by the Galaxy user.
However, the Docker image ought to take care of that - can you give more details of which Docker image you are using (URL, version, etc)?
Thanks,
Peter
On Mon, Aug 14, 2017 at 5:08 PM, Deepak Tanwar <dktanwar@hotmail.commailto:dktanwar@hotmail.com> wrote: Hello everyone,
I am facing problem in uploading bam files on Galaxy. I am using Docker image of Galaxy.
I have installed samtools version 0.1.19 and added it to the path /tool_deps/samtools/0.1.19/iuc/package_samtools_0_1_19/c9bd782f5342/bin/samtools
Error: Exception: Attempting to use functionality requiring samtools, but it cannot be located on Galaxy's PATH.
Thank you, Deepak
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