Running Snakemake pipelines - Revision history

Moiti001: added info on how to install miniconda

2022-01-05T11:25:11Z

added info on how to install miniconda

← Older revision		Revision as of 13:25, 5 January 2022
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	Install <code>conda</code> if you don’t have it		Install <code>conda</code> if you don’t have it
			''Update 05/01/2022:''<br />
			Here I show how to install miniconda in a linux system<br />
			[https://docs.conda.io/en/latest/miniconda.html Download installer]<br />
			[https://conda.io/projects/conda/en/latest/user-guide/install/index.html Installation instructions]

			# Download the installer to your home directory. Choose the version according to your operating system. You can right click the link, copy and download with

			<pre>wget <link></pre>
			At the time of writing this update, for me it would be:

			<pre>wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh</pre>
			To install miniconda, run:

			<pre>bash <installer name></pre>
			installer name could be <code>Miniconda3-latest-Linux-x86_64.sh</code>

			Set up the conda channels in this order:

			<pre>conda config --add channels defaults
			conda config --add channels bioconda
			conda config --add channels conda-forge</pre>

	=== Create conda environment ===		=== Create conda environment ===

Moiti001 at 12:57, 8 October 2021

2021-10-08T12:57:02Z

← Older revision		Revision as of 14:57, 8 October 2021
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	Go to <code>/lustre/nobackup/WUR/ABGC/shared/PIPELINES/</code> and choose which pipeline you want to use.		Go to <code>/lustre/nobackup/WUR/ABGC/shared/PIPELINES/</code> and choose which pipeline you want to use.

	<pre>cp <pipeline directory> <directory where you want to save it to></pre>		<pre>cp -r <pipeline directory> <directory where you want to save it to></pre>
	First you’ll need to do some set up. Go to the pipeline’s directory.		First you’ll need to do some set up. Go to the pipeline’s directory.

Moiti001 at 13:38, 1 July 2021

2021-07-01T13:38:17Z

← Older revision		Revision as of 15:38, 1 July 2021
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	<pre>screen -S <name of session></pre>		<pre>screen -S <name of session></pre>

			You'll need to activate the conda environment again
			<pre>conda activate <name-of-pipeline></pre>

	Then run		Then run

Moiti001 at 08:03, 1 July 2021

2021-07-01T08:03:10Z

← Older revision		Revision as of 10:03, 1 July 2021
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	==== From github ====		==== From github ====

	Go to the repository’s page, click the green “Code” button and copy the path In your terminal go to where you want to download it to and run		Go to the repository’s page, click the green “Code” button and copy the path <br/>
			In your terminal go to where you want to download it to and run

	<pre>git clone <path you copied from github></pre>		<pre>git clone <path you copied from github></pre>

Moiti001 at 06:39, 1 July 2021

2021-07-01T06:39:30Z

← Older revision		Revision as of 08:39, 1 July 2021
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	<pre>snakemake -np</pre>		<pre>snakemake -np</pre>
	This will show you the steps and commands that will be executed. Check the commands and file names to see i		This will show you the steps and commands that will be executed. Check the commands and file names to see if there’s any mistake.

			If all looks ok, you can now run your pipeline

			<pre>snakemake --profile <name-of-pipeline></pre>
			If everything was set up correctly, the jobs should be submitted and you should be able to see the progress of the pipeline in your terminal.

Moiti001: Created page with "Author: Carolina Pita Barros
Contact: carolina.pitabarros@wur.nl
ABG

You can find my pipelines [https://github.com/CarolinaPB/ here] The Snakemake sha..."

2021-06-30T14:24:33Z

Created page with "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG You can find my pipelines [https://github.com/CarolinaPB/ here] The Snakemake sha..."

New page

Author: Carolina Pita Barros 
Contact: carolina.pitabarros@wur.nl 
ABG

 
You can find my pipelines [https://github.com/CarolinaPB/ here]

The Snakemake shared here use modules loaded from the HPC and tools installed with conda.

Click [https://github.com/CarolinaPB/snakemake-template/blob/master/Short%20introduction%20to%20Snakemake.pdf here] for an introduction to Snakemake

== Clone the repository ==

==== From github ====

Go to the repository’s page, click the green “Code” button and copy the path In your terminal go to where you want to download it to and run

<pre>git clone <path you copied from github></pre>
==== From the the WUR HPC (Anunna) ====

Go to <code>/lustre/nobackup/WUR/ABGC/shared/PIPELINES/</code> and choose which pipeline you want to use.

<pre>cp <pipeline directory> <directory where you want to save it to></pre>
First you’ll need to do some set up. Go to the pipeline’s directory.

== Installation ==

Install <code>conda</code> if you don’t have it

=== Create conda environment ===

<pre>conda create --name <name-of-pipeline> --file requirements.txt</pre>
<blockquote>I recommend giving it the same name as the pipeline
</blockquote>
This environment contains snakemake and the other packages that are needed to run the pipeline.

=== Activate environment ===

<pre>conda activate <name-of-pipeline></pre>
=== To deactivate the environment (if you want to leave the conda environment) ===

<pre>conda deactivate</pre>
== File configuration ==

=== Create HPC config file ===

Necessary for snakemake to prepare and send jobs.

==== Start with creating the directory ====

<pre>mkdir -p ~/.config/snakemake/<name-of-pipeline>
cd ~/.config/snakemake/<name-of-pipeline></pre>
==== Create config.yaml and include the following: ====

<blockquote>My pipelines are configured to work with SLURM
</blockquote>
<pre>jobs: 10
cluster: "sbatch -t 1:0:0 --mem=16000 -c 16 --job-name={rule} --exclude=fat001,fat002,fat101,fat100 --output=logs_slurm/{rule}.out --error=logs_slurm/{rule}.err"

use-conda: true</pre>
<blockquote>Here you should configure the resources you want to use.
</blockquote>
=== Go to the pipeline directory and open config.yaml ===

Configure your paths, but keep the variable names that are already in the config file.

<pre>OUTDIR: /path/to/output
READS_DIR: /path/to/reads/
ASSEMBLY: /path/to/assembly
PREFIX: <output name></pre>
If you want the results to be written to this directory (not to a new directory), open the Snakefile and comment out <code>workdir: config["OUTDIR"]</code> and ignore or comment out the <code>OUTDIR: /path/to/output</code> in the config file.

'''Now the setup is complete'''

== How to run the pipeline ==

Since the pipelines can take a while to run, it’s best if you use a [https://linuxize.com/post/how-to-use-linux-screen/ screen session]. By using a screen session, Snakemake stays “active” in the shell while it’s running, there’s no risk of the connection going down and Snakemake stopping.

Start by creating a screen session:

<pre>screen -S <name of session></pre>
Then run

<pre>snakemake -np</pre>
This will show you the steps and commands that will be executed. Check the commands and file names to see i