Skip to content

Latest commit

 

History

History
90 lines (65 loc) · 2.3 KB

installation.md

File metadata and controls

90 lines (65 loc) · 2.3 KB

Installation

BoardION uses the sequencing summary file produced by the basecalling to get metrics on each read. Since this file can be quite large (>10GB), the web application would be slow if it loaded and analyzed it directly. BoardION is therefore divided into two programs :

  • a preprocessing program in C++
  • the web application in R

Docker

A docker image containing both the preprocessing program and the web application is available on docker hub:

docker pull rdbioseq/boardion

See this page for the usage.

Prerequisites

To compile the preprocessing program:

  • gcc>=8.3.0
  • cmake>=2.8

For running the web application:

  • R (tested with R 3.6.0)
  • R packages:
    • bit64
    • data.table
    • plotly
    • shinydashboard
    • shinycssloaders
    • shinyWidgets
    • DT

Install the preprocessing script

First clone the git repository:

git clone https://github.com/institut-de-genomique/BoardION.git
cd BoardION

Compile the preprocessing program ( use '-DCMAKE_INSTALL_PREFIX=' to set the installation path of the binary)

cd preprocess
mkdir build
cd build
cmake -G "Unix Makefiles"  -DCMAKE_INSTALL_PREFIX=path/to/install/dir ..
cmake --build . --target install

This program needs to be executed regularly to update the data displayed in the web interface. For exemple, to execute it every 5 minutes with cron:

crontab -e

add inside the crontab the following line:

*/5 * * * * boardion_preprocess -i input/dir -o output/dir

See here for the complete list of options.

Inside the input directory it will detect and parse every sequencing_summary.txt and final_summary.txt.

Note that the ouput directory needs to be visible by the web server.

Install the web server

The server requires no installation as it is in R but requires several R packages. Therefore an installation with docker or singularity is proposed.

To build the docker in the app folder:

docker build -t boardion-app ./

To build with singularity:

singularity build boardion_app boardion.sif

If you prefer to run it directly on your system, here is the list of dependencies:

  • R (tested with R>=3.6.0)
  • R packages:
install.packages(c("bit64","data.table","plotly","shinydashboard","shinycssloaders","shinyWidgets","DT"))