Platform Preparation

Linux

If you are on a High-Performance Cluster (HPC) or remote server that runs on a Linux OS, like Ubuntu or Red Hat for example, then please follow the instructions on the previous Installation page!



Windows / PC

  • Step 1. Freely download the UBUNTU app from the Windows store

  • Step 2. Open the UBUNTU app and create a username and pw

  • Step 3. Run the following:

obtain mamba package manager:

curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"

install mambaforge (type ‘yes’ to all interactive prompts)

bash Mambaforge-$(uname)-$(uname -m).sh

  • Step 4. RESTART

  • Step 5. Install Singularity following the instructions on the Installation page.

  • Step 6. Install conda environment for Iliad which contains Snakemake

mamba create -c conda-forge -c bioconda --name iliadEnv snakemake snakedeploy openpyxl

  • Step 7. Change directories in the UBUNTU command line to get into proper location of your project folder

cd mnt/DRIVE/Path/To/Iliad/

  • Step 8. Activate your conda environment (IliadEnv)

Mamba activate IliadEnv

  • Step 9. Get your current location to add to the configuration file

pwd

  • Step 10. Copy that location and paste into the Iliad/config/config.yaml as your working directory. This should start with /mnt/ and end with a forward slash / like so /mnt/Drive/Path/To/Iliad/



MacOS

  • Step 1. Download the latest version of Oracle VM VirtualBox <”https://www.oracle.com/virtualization/technologies/vm/downloads/virtualbox-downloads.html#vbox”>_.

  • Step 2. Use the GUI - there is an easy install that makes editing a virtual machine in the mac quite simple. This required since Singularity needs to run on Linux.

  • Step 3. Use a pre-made singularity container on sylabs

export VM=sylabs/singularity-ce-3.8-ubuntu-bionic64 && \
vagrant init $VM && \
vagrant up && \
vagrant ssh

  • Step 4. Gain control through the virtal machine application. This removes the need to go editing the vagrantfile.

  • Step 5. Increase your storage space alotted for the virtual machine.