From 301523d5988e0937a2cf6eea0274794f20e5938f Mon Sep 17 00:00:00 2001 From: frank Date: Tue, 1 Mar 2022 20:15:01 -0500 Subject: [PATCH] first commit --- README.md | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 README.md diff --git a/README.md b/README.md new file mode 100644 index 0000000..b395eb4 --- /dev/null +++ b/README.md @@ -0,0 +1,41 @@ +# Nextflow getting started + +--- +## Before Getting Started + +#### Windows Users +You should havve Windows Subsystem for Linux (WSL2) installed with a version of linux. My recommendation is that your version of linux should be `Ubuntu 20.04` because you will find more help online when you search for linux help. If you don't already have WSL2 installed, follow these directions to [install WSL2 on Windows 10](https://youtu.be/n-J9438Mv-s?t=51). Once you have a linux terminal open, you can follow any linux guide online because you are now using linux (as a virtual machine on your windows computer). Java is part of the default installation of Ubuntu 20.04 so you should be all set to install nextflow. + +#### Mac Users +You will need to [install Java](https://devqa.io/brew-install-java/) because it's not part of the default installation of MacOS. To check if you installed Java previously, open a terminal window and type `java -version` and if you have it installed, you'll see which version is available. + +--- +### Prerequisites +1. Java version 8 or later + - You can check by running `java -version` at the terminal. (If your output is `openjdk version 1.8.xxx` this is version 8. If you want to read more about why, here's a [link with more info](https://www.quora.com/Do-Java-1-8-and-Java-8-refer-to-the-same-thing). + + +### Installing Nextflow + +1. Open a terminal window or (logon to `Xanadu`). +2. You should already be in your home directory but you can type `cd ~` or simply `cd` will also take you to your home directory. +3. Create a directory called `nextflow` and change directory to this new directory. + - `mkdir nextflow && cd nextflow` +4. Download and execute the nextflow install file by typing the following into your terminal. + - `curl -s https://get.nextflow.io | bash` + +You can now run nextflow. Let's check the version by typing +- `./nextflow -version`. + +But this is inconvenient because if you try to run nextflow from a different directory, you will need to type `~/nextflow/nextflow -version` so let's create a symlink so that we can use a shortcut. Type + +- `sudo ln -s ~/nextflow/nextflow /usr/local/bin/` + - (on `Xanadu` you might not need to use `sudo`) + +The `ln` command is a useful command to know so you might want to [read more about it](https://linuxize.com/post/how-to-create-symbolic-links-in-linux-using-the-ln-command/). + +Now you can just type `nextflow -version` from any directory. Nextflow comes with a hello world pipeline ready to run so let's run our first pipeline! + +- `nextflow run hello` + +The output of your pipeline should be "hello world" four times each in a different language. \ No newline at end of file