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Commit e92f4c2d authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion :recycle:
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Merge branch 'sunbeam' into 'master'

add documentation for sunbeam

Closes #8

See merge request !2
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1 merge request!2add documentation for sunbeam
...@@ -5,6 +5,7 @@ ...@@ -5,6 +5,7 @@
Name | Description Name | Description
---- | ----------- ---- | -----------
[Data simulation](simulation/) | Generate simulated metagenomics data for benchmarking [Data simulation](simulation/) | Generate simulated metagenomics data for benchmarking
[Sunbeam](sunbeam/) | How to use sunbeam at Pasteur on TARS
## Projects and repository ## Projects and repository
......
...@@ -24,6 +24,9 @@ make the process a bit faster. Files can be found in the `example/` directory. ...@@ -24,6 +24,9 @@ make the process a bit faster. Files can be found in the `example/` directory.
All the path are preceded by the `/input` directory since we are going to mount our config All the path are preceded by the `/input` directory since we are going to mount our config
files into this directory. files into this directory.
> **Warning** Generated paired-end reads are in one unique `fastq` file that need to be
splitted in `_R1` and `_R2` files.
### With docker ### With docker
```bash ```bash
...@@ -71,13 +74,10 @@ output_directory=out ...@@ -71,13 +74,10 @@ output_directory=out
temp_directory=/tmp temp_directory=/tmp
gsa=True # whether a gold standard assembly should be created gsa=True # whether a gold standard assembly should be created
pooled_gsa=True # whether a pooled gold standard over all samples is created pooled_gsa=True # whether a pooled gold standard over all samples is created
anonymous=False # whether the output is anonymized anonymous=True # whether the output is anonymized (reads from genomes are shuffled)
compress=1 # 0 is for no compression, 9 is maximum compression compress=1 # 0 is for no compression, 9 is maximum compression
``` ```
Since we do not need the data for a challenge, we can switch off the anonymous part of the process. _For the moment it seems that it [does not work without anonymization]
(https://github.com/CAMI-challenge/CAMISIM/issues/64) so it is better to keep the `anonymous` flag to `True`_.
#### Read Simulator #### Read Simulator
```ini ```ini
......
# Sunbeam
[Sunbeam](https://github.com/sunbeam-labs/sunbeam) is a pipeline written in snakemake
that simplifies and automates many of the steps in metagenomic sequencing analysis.
Here is a brief note to help you use sunbeam at Pasteur on TARS. You can also read the
full [documentation](https://sunbeam.readthedocs.io/en/latest/?badge=latest).
## Install
Procedure is very similar to what you would do locally. Install deal with conda install
if you are not using conda. If you want the latest available version:
```bash
git clone https://github.com/eclarke/sunbeam
cd sunbeam
bash install.sh
source activate sunbeam
```
> **Warning** You need internet access to do that so you need to perform install on
the head of submission.
## Run sunbeam
You can follow the [documentation](https://sunbeam.readthedocs.io/en/latest/?badge=latest)
for the initialization of your analysis directory. This will generate a config file in this
directory that we will call `sunbeam_config.yml`.
We also consider that we are working on the dedicated `atm` queue.
Once done you can run sunbeam for the quality control on tars:
```bash
sbatch --qos=atm -p atm -c 1 sunbeam run --configfile sunbeam_config.yml all_qc --jobs 10 --cluster-config cluster.yml --cluster "sbatch --qos=atm -p atm -c {threads}"
```
Refer to the [documentation](https://sunbeam.readthedocs.io/en/latest/?badge=latest) to
see all the different pipelines available.
You can also personalize required resources by adding a `cluster.yml` file as described in
this [page](https://gitlab.pasteur.fr/metagenomics/snakemake/tree/master/workflows#using-on-tars)
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