Re: [galaxy-dev] Samtools problem in Docker

Hi Deepak, this is still strange. But as a general remark, don't try to install package_samtools_1_2 or package_* these are deprecated in favor of Conda packages. Glad it is working now for you! Ciao, Bjoern On 15.08.2017 16:31, Deepak Tanwar wrote: > Hi Björn, > > I tried again from scratch.

Re: [galaxy-dev] Samtools problem in Docker

Hi Björn, I tried again from scratch. 1. I have installed galaxy-stable image via Kitematic. 2. I install samtools: package_samtools_1_2 (2015-07-17) iuc 3. I have uploaded the bam file. Error: Traceback (most recent call last): File "/galaxy-central/tools/data_source/upload.py", line 425,

Re: [galaxy-dev] Samtools problem in Docker

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

Re: [galaxy-dev] Samtools problem in Docker

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 > wrote: Galaxy

Re: [galaxy-dev] Samtools problem in Docker

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,

[galaxy-dev] Samtools problem in Docker

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