Added Xanadu specific instructions

Xanadu specific instructions and rnatoy pipeline

README.md

@@ -15,9 +15,9 @@ You will need to [install Java](https://devqa.io/brew-install-java/) because it'
     - 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
+### Installing Nextflow (local computer)
 
-1. Open a terminal window or (logon to `Xanadu`).
+1. Open a terminal window.
 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`
@@ -30,12 +30,49 @@ You can now run nextflow. Let's check the version by typing
 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/).
 
+### Installing Nextflow on Xanadu
+1. Start an interactive session to keep the admins happy.
+    - `srun -p general -q general -t 4:00:00 --mem 4G --pty bash`
+2. Create an `opt` directory in your home directory and change directory into this new directory.
+    - `mkdir -p ~/opt && cd ~/opt`   
+3. Download and install the nextflow install script.
+    - `curl -s https://get.nextflow.io | bash`
+
+Add the path to the `opt` directory to your `PATH`
+
+4. Open your `.bashrc` file using `vim` or `nano`.
+5. Add the following line to the end of your `.bashrc` file.
+    - `export PATH="/home/FCAM/$USER/opt/:$PATH"`
+6. Source your `.bashrc` so the change takes effect.
+    - `source ~/.bashrc`
+7. Check if the new `opt` directory is in your `PATH`.
+    - `echo $PATH | grep "$USER/opt"`
+    - You should see your username and opt in red
+
+### Running Nextflow
+
 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.
+The output of your pipeline should be "hello world" four times each in a different language.
+
+---
+
+### Running Nextflow RNAtoy pipeline on Xanadu
+
+If you haven't already done so, start an interactive session `srun -p general -q general -t 4:00:00 -c 4 --mem 8G --pty bash`
+
+1. Create a `nextflow_pipelines` directory in your home directory and change into this directory
+    - `mkdir -p ~/nextflow_pipelines && cd ~/nextflow_pipelines`
+2. Clone the `rnatoy` repo and change into this direcotry.
+    - `git clone https://github.com/nextflow-io/rnatoy.git && cd rnatoy`
+3. Load singularity
+    - `module load singularity`
+4. Pull the needed docker container
+    - `singularity pull docker://nextflow/rnatoy:1.3`
+5. Run the rnatoy pipeline using a singularity container
+    - `nextflow run main.nf -with-singularity rnatoy_1.3.sif`