Installation

Installation via GitHub/pip

Download the SPECIMEN repository here and run the command pip install -e . inside the top-level directory.

Hint

To additionally install all packages necessary for working with the docs, install the tool with the extra docs, e.g.

pip install -e ".[docs]" --config-settings editable_mode=strict

For all options to run error-free, the following tools need to be installed additionally:

• DIAMOND, version 2.0.4 or higher

• EntrezDirect, if no NCBI mapping has been created beforehand

Afterwards, SPECIMEN can either be accessed via the command line or via importing the package into a Python script.

SPECIMEN can also be used via Docker. To build the docker image, firtsly clone the repository:

git clone "https://github.com/draeger-lab/specimen.git"

Then change into the directory and build the image:

cd specimen \
docker build -t specimen .

Note

To provide the input files and retrieve the output files mount one folder as workspace folder to the Docker image with -v.

The default command executed by the image is specimen -h and provides the help information for the CLI of SPECIMEN.

docker run specimen

To use the image interactively and open a bash shell, run the following command:

docker run -it --entrypoint bash specimen

To use the image for specific commands, you can simply use every of the CLI commands as entrypoint. For example, to run the CMPB pipeline, use:

docker run --name <container_name> -v <user_folder>:/sp_cont specimen cmpb run ./path/to/CMPB_config.yaml

Hint

It is advised to install SPECIMEN inside a conda environment with a Python version of 3.10 or higher.