Accessing bwa mem inside docker.

[kghimire09]

Hi biodocker team,  I am building a fastq to vcf pipeline using bwa, gatk and picard tools. I implemented your code for docker image for bwa, gatk and picard. For bwa I used  From biocontainers/biocontainers:latest The metadata Installation RUN conda install bwa=0.7.15.  Now that issue I have is how do I run the bwa commands to build my script? I need to use bwa mem command. Same with gatk and picard. Please could you help me? Thank you

[osallou]

Why do you build a container with all tools and not simply call in your script each tool container?

I do not really understand your issue. If you conda installed bwa etc... when running your container you should just need to call executable names in your docker run

[bgruening]

Please let us know if you have still problems. Closing for now.