Assume "yes" as the answer to any prompts with bioconda

Question

[njornet]

I'm generating a docker container to run my program and I have to download a series of packages. Is there any flags to make bioconda assume yes, similar to "apt install -y"? Also, is there any way to install several packages in the same line or do I have to write "RUN conda install bioconda::package" in a separate line for each package?

Thank you!

Answer 1

[Juke34]

From my experience using biocontainers base container no need to set yes installation is done without any command prompt, otherwise as for apt install use the flag -y it works (maybe depend the version of conda...).
So to install several tools you can do something like that to variate Chanels

# add dependencies via conda
RUN conda install -c bioconda samtools && \
         conda install -c anaconda python && \
         conda install  r-base

If you have many dependencies you can list them in a yaml file e.g. dep.yml:

name: base
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - tool1
  - tool2=versionX
  - tool3

and then in your Dockerfile you do:

# copy YML dependency file
COPY dep.yml /tmp/dep.yml

# Install dependencies listed in dep.yml  file
RUN conda env update -n base --file /tmp/dep.yml

Answer 2

[Dave Carlson]

conda install -y bioconda::packageX conda-forge::packageY should do what you're looking for.