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Getting started

The quickest way to install and use BlobToolKit is using pip install. We recommend first setting up a new conda environment with python=3.9. The advantage of conda is that everything can be installed in a separate user directory, even on a cluster, without affecting anything else installed.

## Install Conda

Conda can be installed on the command line using the Miniconda installer:

curl -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh > Miniconda3.sh; chmod +x Miniconda3.sh; ./Miniconda3.sh

N.B. you will need to open a new terminal window before using conda as the commands will not be available in the current session

Install BlobToolKit

To create and activate a new conda environment called btk with python=3.9:

conda create -y -n btk -c conda-forge python=3.9
conda activate btk

To install blobtoolkit:

pip install "blobtoolkit[full]"

For a more compact install (without pipeline or viewer hosting options) use:

pip install blobtoolkit

To test that the installation worked, type blobtools -h and you should see the help text for that command.