Installation¶
Install the pipline and the dependencies using conda¶
Tip
If you plan to use the docker image, you can skip this section.
immunopipe is built upon pipen framework, and a number of packages written in R and python. It's not recommended to install the packages manually. Instead, you can use the provided environment.yml to create a conda environment.
$ conda env create \
-n immunopipe \
-f https://raw.githubusercontent.com/pwwang/immunopipe/master/docker/environment.yml
Attention
The environment.yml includes only a subset of the packages required by the pipeline. The dependencies of the TESSA process are not included.
If you want to enable TESSA process , please use the environment_full.yml (https://raw.githubusercontent.com/pwwang/immunopipe/master/docker/environment_full.yml) instead.
See also Choose the right tag of the docker image.
If the URL doesn't work, you can download the file and create the environment locally.
For more detailed instructions of conda env create, please refer to conda docs.
Attention
The pipeline itself is NOT included in the conda environment. You need to install it separately.
$ conda activate immunopipe
$ pip install -U immunopipe
$ # If you want to create diagram and generate running information
$ pip install -U immunopipe[diagram,runinfo]
$ # You also need to install the frontend dependencies to generate reports
$ pipen report update
Use the docker image¶
You can also use the docker image to run the pipeline. The image is built upon miniconda3 and micromamba is used as the package manager. The image is available at Docker Hub.
To pull the image:
$ docker pull justold/immunopipe:<tag>
If you are using singularity, you can pull and convert the image to sif format:
$ singularity pull docker://justold/immunopipe:<tag>
$ apptainer pull docker://justold/immunopipe:<tag>
To run the pipeline use the image, please refer to Running the pipeline.
The directory structure in the container¶
The docker image is build upon mambaorg/micromamba:1.4.3. The OS is linux/amd64. Other than the default directories, the following directories are also created or should be mapped during the run:
/immunopipe: The directory where the source code of the pipeline is. It is general a clone of the repository. The pipeline is also installed from this directory./workdir: The working directory. It is the directory where the pipeline is run. It is recommended to map the current directory (.) to this directory./data: An empty directory. You can map your data directory to this directory.