diff --git a/README.md b/README.md index b395eb4..73a6e0a 100644 --- a/README.md +++ b/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. \ No newline at end of file +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`