Initialization: Bash Script¶

For any app with a Bash shell, a bash script can be loaded (*.sh) during app initialization using the optional parameter Initialization.

The bash script should include a shebang (#!/usr/bin/env bash) and have the .sh file extension.

The script will be executed when the app is initialized, and can be used to install relevant packages or configuration.

The script in the first tab (Installing R-packages) includes the installation of R packages. The second and the third tab show how to install the mariadb-server, with the apt package manager (for Debian/Ubuntu based distributions) or with the yum package manger (for Red Hat based distributions), respectively.

Example bash scripts:

Installing R-packages

#!/bin/bash

sudo apt-get update
sudo apt-get install -y libssl-dev liblzma-dev libbz2-dev libicu-dev libxml2-dev libglpk-dev
sudo apt-get clean

R -e "install.packages('BiocManager', repos='http://cran.us.r-project.org'); \
    update.packages(ask=F); \
    BiocManager::install(ask=F); \
    BiocManager::install(c('dplyr','plotly'),ask=F)"

R -e "library(BiocManager); BiocManager::install(c('matrixStats','igraph','parallel', \
    'lattice','plyr','gplots','data.table','clusterProfiler','org.Hs.eg.db','STRINGdb', \
    'jsonlite','shinydashboard','shinyBS'    ,'limma'),ask=F)"

R -e "library(BiocManager); BiocManager::install(c('biomaRt'),ask=F)"

using apt

#!/usr/bin/env bash
sudo apt update
sudo apt install -y mariadb-server

using yum

#!/usr/bin/env bash
sudo yum install -y mariadb-server

Note

Please note that for some apps, this option might be called Dependencies or Additional Dependencies.