poeli/pangia repository overview

⁠PanGIA Docker

PanGIA is a bioinformatics pathogen detection software for the End-to-End Whole Genome Sequencing diagnostic system. This docker container runs PanGIA-UI that provides a web-based GUI to facilitate users to analyze their datasets through PanGIA and access to results.

⁠Launch PanGIA Docker

1. Creating resource directories for input, output and database:

   # for example, "pangia_input", "pangia_output" and "pangia_database"
   mkdir pangia_input pangia_output pangia_database
   

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2. Specifying ABSOLUTE paths of resource directories to mount on the container and a local port:

   # specify directories and a local port
   PANGIA_INPUT=$(pwd)/pangia_input
   PANGIA_OUTPUT=$(pwd)/pangia_output
   PANGIA_DATABASE=$(pwd)/pangia_database
   PANGIA_LOCAL_PORT=8080
   

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3. Run commands:

   # create mysql volumn
   docker create --name mysql_data_pangia --volume /var/lib/mysql bioedge/edge_mariadb
   
   # pull docker
   docker pull poeli/pangia
   
   # launch pangia docker
   docker run -d --restart always \
       --privileged=true \
       --security-opt "seccomp:unconfined" \
       --cap-add=SYS_ADMIN \
       --cap-add=SYS_PTRACE \
       --volumes-from mysql_data_pangia \
       -v $PANGIA_INPUT:/home/edge/EDGE_input \
       -v $PANGIA_OUTPUT:/home/edge/EDGE_output \
       -v $PANGIA_DATABASE:/home/edge/database \
       -p $PANGIA_LOCAL_PORT:80 \
       --name pangia\
       poeli/pangia
   

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4. Download databases:

   # run "pangia_db_update" command in the container
   docker exec pangia pangia_db_update
   

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5. Open browser and goto localhost:8080.

⁠Update PanGIA Docker

1. Stopping and removing current container:

   # stop and remove the container
   docker stop pangia
   docker rm pangia
   

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2. Pulling PanGIA container

   # pull latest docker
   docker pull poeli/pangia
   

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3. Launching PanGIA Docker again with docker run command (see Launch PanGIA Docker - 2)).

4. Checking if local database is compatible with latest container:

   # run pangia_db_update with "--checkOnly" option to check the compatibility of the database
   docker exec pangia pangia_db_update --checkOnly
   # or, use pangia_db_update directly to retrieve updated databases.
   docker exec pangia pangia_db_update
   

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5. You are good to go!