From b124dd7ecfb06679dd49b188ca65c62760b7812c Mon Sep 17 00:00:00 2001 From: Hugo Tavares Date: Tue, 8 Aug 2023 11:45:52 +0100 Subject: [PATCH] update setup instructions --- 101-setup.md | 27 ++++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/101-setup.md b/101-setup.md index 3edbd5e..f3546ac 100644 --- a/101-setup.md +++ b/101-setup.md @@ -36,9 +36,12 @@ The **Windows Subsystem for Linux (WSL2)** runs a compiled version of Ubuntu nat There are detailed instructions on how to install WSL on the [Microsoft documentation page](https://learn.microsoft.com/en-us/windows/wsl/install). But briefly: -- Click the Windows key and search for _Windows PowerShell_, open it and run the command: `wsl --install`. -- Restart your computer. -- Click the Windows key and search for _Ubuntu_, which should open a new terminal. +- Click the Windows key and search for _Windows PowerShell_, right-click on the app and choose **Run as administrator** +- Answer "Yes" when it asks if you want the App to make changes on your computer. +- A terminal will open; run the command: `wsl --install`. + - This should start installing "ubuntu" + - It may ask for you to restart your computer. +- After restart, click the Windows key and search for _Ubuntu_, click on the App ant it should open a new terminal. - Follow the instructions to create a username and password (you can use the same username and password that you have on Windows, or a different one - it's your choice). - You should now have access to a Ubuntu Linux terminal. This (mostly) behaves like a regular Ubuntu terminal, and you can install apps using the `sudo apt install` command as usual. @@ -76,9 +79,22 @@ sudo apt install -y default-jre ## Software Setup -### _Conda_ +### _Conda_ We recommend using the _Conda_ package manager to install your software. +In particular, the newest implementation called _Mamba_. + +To install _Mamba_, run the following commands from the terminal: + +```bash +wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh" +bash Mambaforge-$(uname)-$(uname -m).sh -b +rm Mambaforge-$(uname)-$(uname -m).sh +``` + +Restart your terminal (or open a new one) and confirm that your shell now starts with the word `(base)`. + +
Old instructions To install _Conda_, run the following commands from the terminal: ```bash @@ -97,7 +113,7 @@ We also install the `mamba` package, which is a faster implementation of the `co ```bash conda install -y mamba ``` - +
### Singularity @@ -122,6 +138,7 @@ You can do that with the following command: ```bash mamba create -n nextflow -y nextflow +mkdir $HOME/.nextflow ``` When you want to use _Nextflow_ make sure to activate this software environment by running `conda activate nextflow`.