README.md

Run PAPipe with a small test data

1. Installing the Docker Engine (Need root permission)

Skip if your machine already has the engine (Installation document).

curl -fsSL https://get.docker.com/ | sudo sh

2. Adding a Docker user to the docker group (Need root permission)

Skip if your account is already in the docker group

sudo usermod -aG docker $USER 	

3. Downloading and loading the Docker image file

wget http://bioinfo.konkuk.ac.kr/PAPipe/PAPipe.tar.gz    # Download the Docker image file
docker load -i ./PAPipe.tar.gz    # Load the Docker image file
docker image ls    # Check if the image loaded well ("REPOSITORY:pap_docker, TAG:latest" must be shown)

4. Downloading the test data

wget http://bioinfo.konkuk.ac.kr/PAPipe/test_data.tar.gz
tar -zxvf test_data.tar.gz

5. Creating a docker container that mounts the directory containing the test data

Need to use the absolute path of the "test_data" directory.

docker run -v [absolute path of the "test_data" directory]:/RUN_DOCKER/  -it pap_docker:latest

6. Running PAPipe in the Docker container

# Run in the docker container
cd /RUN_DOCKER
python3 /PAPipe/bin/main.py  -P ./main_param.txt  -I ./main_input.txt -A ./main_sample.txt &> ./log

7. Generating HTML pages for browsing analysis results

# Run in the docker container
perl /PAPipe/bin/html/webEnvSet.pl ./out &> webenvset.log # ./out is the output directory set in the "main_param.txt" file
cd ./out/web/
perl /PAPipe/bin/html/prep_html.pl ./ &> ./webgen.log

Example HTML pages for browsing the results

Check out the HTML pages generated by this test data here.