mouse-pergola-reproduce.nf

This repository contains the software, scripts and data to reproduce the results corresponding to the CB1 mice experiment of the Pergola paper.

If you have not install yet docker and nextflow, follow this intructions

Clone the repository

git clone --recursive https://github.com/JoseEspinosa/mouse-pergola-reproduce.git
cd mouse-pergola-reproduce

Data

Data is publicly available in Zenodo as a compressed tarball.

Data can be downloaded and uncompressed using the following command:

mkdir data
wget -O- https://zenodo.org/record/580312/files/mouse_dataset.tar.gz | tar xz -C data

Pull docker image

Pull the Docker image use for processing data with Pergola (Pergola and its dependencies installed)

docker pull pergola/pergola@sha256:f7208e45e761dc0cfd3e3915237eb1a96eead6dfa9c8f3a5b2414de9b8df3a3d

Run nextflow pipeline

Once data is downloaded, it is possible to reproduce all the results using this command:

NXF_VER=0.26.1 nextflow run mouse-pergola-reproduce.nf \
  --recordings='data/mouse_recordings/' \
  --mappings='data/mappings/b2p.txt' \
  --mappings_bed='data/mappings/bed2pergola.txt' \
  --phases='data/phases/exp_phases.csv' \
  --mappings_phase='data/mappings/f2g.txt' \
  --exp_info='data/mappings/exp_info.txt' \
  --image_format='tiff' \
  -with-docker

Online visualization

Downloading shiny-pergola config file

Download the configuration files assigning files to each of the group (wt_food_sc, wt_food_fat, cb1_food_sc, cb1_food_fat)

wget -O-  https://gist.githubusercontent.com/JoseEspinosa/9e65d54d765d9e5af554d837b3427569/raw/48fb424fb367c570461e7e6c8226abf81ead8ee2/cb1_pergola_conf.txt > exp_info.txt

Downloading and running the shiny-pergola image

Pull the docker image containing the version of shiny-pergola web application used for render the data visualization:

docker pull pergola/shiny-pergola@sha256:e8791c5f230b612a6f702ac397849163e3a52b923befd1977e4a4c0235e91f72

With docker running, launch the image:

docker run --rm -p 3600:80 -v "$(pwd)":/pergola_data  pergola/shiny-pergola@sha256:e8791c5f230b612a6f702ac397849163e3a52b923befd1977e4a4c0235e91f72 &

Note: "$(pwd)" can be substitute by your absolute path to the folder where the mouse-pergola-reproduce.nf has been run.

Note: Figure has several snapshots if you want to get exactly the exact the same figure just select it by setting on id.txt file. For instance if you want to reproduce figure a you just have to type the following command before running Docker shiny-pergola image.

echo "cb1_a" > id.txt

Go to your web browser and type in your address bar the ip address returned by the following command e.g. http://0.0.0.0:3600

Note: In newer Docker versions by default the IP address used is the localhost 0.0.0.0. As this IP might be used by other services in the default port (80), we especified the port used in our docker command by -p 3600:80. Old docker versions running in OS might used a different IP address that you can get using the following command (usually this one http://192.168.99.100). You may then enter this IP followed by the same port in the address bar of your browser http://192.168.99.100:3600.

docker-machine ip default 

Et voila, the running container will load the shiny app in your browser.