To create a Dockerfile that uses conda to install samtools, you can use the following steps:
Start by creating a new file called Dockerfile in your working directory.
In the Dockerfile, specify the base image that you want to use.
Note A Docker base image is a starting point for creating Docker containers. It includes the basic elements and libraries necessary for running a container, such as the operating system and common software packages. Base images are typically created by organizations or individuals and made available for use by the Docker community. They can be customized and built upon to create specific applications or services.
This can be any image that includes the conda package manager, such as the continuumio/miniconda3 image.
For example:
FROM continuumio/miniconda3
Next, run the conda command to create a new conda environment and install the samtools package. This can be done in a single RUN command, as follows:
RUN conda create -n samtools-env samtools
This will create a new conda environment called samtools-env and install the samtools package within it.
After the environment is created and the samtools package is installed, you can activate the environment using the conda activate command.
This can be done in a separate RUN command, as follows:
RUN conda activate samtools-env
Finally, you can specify the default command that should be run when the Docker container is started.
This can be the samtools command, for example:
CMD ["samtools"]
Your complete Dockerfile should look something like this:
FROM continuumio/miniconda3
RUN conda create -n samtools samtools
RUN conda activate samtools
CMD ["samtools"]
Once you have created the Dockerfile, you can build the Docker image by running the docker build command and specifying the path to the Dockerfile.
For example:
$ docker build -t samtools:1.16.1 .
This will create a new Docker image called my-samtools-image
that includes the samtools package and is ready to use.
You can then run a Docker container using this image by running the docker run command, as follows:
$ docker run -it my-samtools-image
This will start a new Docker container based on the my-samtools-image image and run the default samtools command.
You can then use the samtools command as you normally would within the Docker container.
To publish image to Docker hub
docker login -u <username> -p <password>
docker tag <image name>:<tag> <username>/<image name>:<tag>
docker push <username>/<image name>:<tag>
singularity build <image name>.sif docker://<username>/<image name>:<tag>
You can specify the conda environment in a file and use this to create the environment
In the same working directory as the Dockefile add the copy statement for the environment.yaml file
COPY environment.yaml /tmp/environment.yaml
RUN conda env create -f /tmp/environment.yaml
Activate the conda environment
RUN echo "source activate <environment name>" > ~/.bashrc
ENV PATH /opt/conda/envs/<environment name>/bin:$PATH
https://pythonspeed.com/articles/conda-docker-image-size/