How to install

Gempipe is developed and tested under linux/amd64.

conda (recommended)

Gempipe can be easily installed via conda:

conda install gempipe -c bioconda -c conda-forge --no-channel-priority

💡 Tip! In case a fresh new, dedicated environment for Gempipe is needed, just type conda create -n gempipe_env gempipe -c bioconda -c conda-forge --no-channel-priority, then activate it with conda activate gempipe_env to use Gempipe.

💡 Tip! mamba is a drop-in replacement for conda, but much more fast! Once mamba is installed, mamba install gempipe -c bioconda -c conda-forge --no-channel-priority will take less time then the conda counterpart.

📌 Note! The Gempipe conda package is signed as “noarch” (architecture independent), but its dependencies may not be available for all platforms. For example, cd-hit is currently still not available for recent Apple Silicon (ie osx-arm64) machines, so the installation on this architecture will be halted; older Intel-based Apple machines (osx-64) should not have any problems.

📌 Note! The --no-channel-priority option is needed since biopython is no more updated in bionconda, so the dependency biopython>=1.80 can be satisfied only through conda-forge.

Docker

To get the exact same environment used during the Gempipe development, use the dedicated Docker image. To run the container, please refer to the Jupyter Docker Stacks documentation.