Hi Deepak, as Peter mentioned the Galaxy Docker container can be used as it is. Can you provide the original error message from the TS?
Cheers, Bjoern On 14.08.2017 18:17, Deepak Tanwar wrote: > 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.c...@googlemail.com >> <mailto:p.j.a.c...@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 <dktan...@hotmail.com >> <mailto:dktan...@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 >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/ > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
