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VM Installation

Install script

Things to include:

  • Logging
  • Setting directory permissions
  • Checking required network access
  • Check available disk
  • Automated testing to ensure things are set up correctly, e.g.
    • Permissions
    • Install success
    • Use 0 vs non-0 exit status
  • Automated cleanup
  • Setting and verifying environmental variables
  • Checking data integrity (checksums)

Usage

cd $HOME
git clone https://github.com/Sydney-Informatics-Hub/hello-nextflow.git

# Sort out docker groups before installation 
uname=user1
sudo adduser $uname
if ! getent group docker; then
    sudo groupadd docker
fi
sudo usermod -aG $USER
sudo usermod -aG $uname
newgrp docker # not sure if this is needed if rebooting
sudo reboot

# Install and validate for root user, set docker permissions for user
bash hello-nextflow/vm_install/ubuntu_install.sh $uname

# Test installs for user
sudo su - $uname

## utils
tree
tr

## nextflow
nextflow run nextflow-io/hello # in $HOME
rm -rfv .nextflow* work/

## docker
docker run "quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0"
docker run "quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
docker run "quay.io/biocontainers/multiqc:1.19--pyhdfd78af_0"

# Set dir structure and get files required for the workshop (in user1)
cd $HOME
git clone https://github.com/Sydney-Informatics-Hub/hello-nextflow.git
cp -r hello-nextflow/part1 hello-nextflow/part2
rm -rfv hello-nextflow/