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install_seqnado.sh
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install_seqnado.sh
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#!/bin/bash
if ! command -v mamba &> /dev/null; then
echo "mamba not found. Installing mambaforge..."
# Install mambaforge using the official installer
wget https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh -O mambaforge.sh
bash mambaforge.sh -b -p $HOME/mambaforge
rm mambaforge.sh
# Add mambaforge to the PATH
export PATH="$HOME/mambaforge/bin:$PATH"
fi
# Create a new conda environment
echo "Creating a new conda environment..."
mamba create -n seqnado_dev "python>=3.12" pip -y
# Activate the conda environment
echo "Activating the conda environment..."
conda activate seqnado_dev
# Install the seqnado package using pip
echo "Installing seqnado..."
pip install seqnado
# Deactivate the conda environment
echo "Deactivating the conda environment..."
conda activate base
# Set the environment variables for CCB
if [[ $(hostname) =~ "imm-" ]]; then
echo export APPTAINER_BINDPATH="/ceph:/ceph, /project:/project, /databank:/databank" >> ~/.bashrc
export APPTAINER_BINDPATH="/ceph:/ceph, /project:/project, /databank:/databank"
fi
echo "Done!"