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Server setup

Setup conda for all users

cd /opt
sudo wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
sudo chmod +x Miniconda3-py39_4.12.0-Linux-x86_64.sh
sudo ./Miniconda3-py39_4.12.0-Linux-x86_64.sh
sudo groupadd condausers
sudo chgrp -R condausers /opt/miniconda3/
sudo chmod 775 -R /opt/miniconda3/
sudo chown -R :condausers /mnt/lfw-ds001-v019/data
sudo chmod -R 775 /mnt/lfw-ds001-v019/data

Create a user account

  • Create a user
sudo adduser testuser
sudo adduser testuser condausers
  • Add to /home/testuser/.bashrc:
export PATH="/opt/miniconda3:$PATH"
  • Conda init:
su - testuser
conda init
  • Install the pipeline
git clone https://github.com/iobis/PacMAN-pipeline.git
  • Link to the shared databases
cd PacMAN-pipeline
ln -s /home/ubuntu/data/databases/ data/databases
  • Add to /home/testuser/.bashrc:
cd PacMAN-pipeline
conda activate snakemake

Connecting using Visual Studio Code

  • Install Visual Studio Code from https://visualstudio.microsoft.com/.
  • In Visual Studio, install the Remote Explorer extension from Microsoft.
  • In Remote Explorer, add a new target:
ssh [email protected]
  • Then connect to the newly created SSH target and enter your password
  • You can now open your folder /home/testuser/PacMAN-pipeline in the Explorer

Running the pipeline

  • Click pipeline in the NPM scripts panel on the bottom left