temporary location for a dockerfile for indeXplorer

first clone this git repo you see here

next change to this dir

cd indeXplorer-docker

then clone indeXplorer inside the indeXplorer-docker dir using

git clone https://git.embl.de/velten/indeXplorer.git

then build docker image

docker build .

in order we can run the web app, we need to put some data in a specific folder and define this folder as a docker run(time) argument

for example define the following location on your host system

mkdir ~/indeXplorer_data
DATA_DIR=~/indeXplorer_data

copy some example data in it

cd $DATA_DIR
wget http://steinmetzlab.embl.de/shiny/indexplorer/data.zip
unzip -j data.zip

now run the container defining the local folder (providing a local folder is mandantory, otherwise the shiny webapp indeXplorer will throw an error when startin g) first do a test

if ! [ -f $DATA_DIR/MASTER_ALL.rda ]; then echo "mandantory file for indeXplorer not found!"; fi

then run the app

docker run --rm -p 80:3838 -v $DATA_DIR:/data indeXplorer

following options are defined on running docker

verbose_logfiles creates extensive log files in /var/log/shiny-server

verbose_logfiles=[TRUE,FALSE] 

e.g.

docker run --rm -p 80:3838 -e verbose_logfiles=TRUE -v $DATA_DIR:/data indeXplorer

behind a webproxy use the following

websockets_behind_proxy=TRUE

e.g.

docker run --rm -p 80:3838 -e verbose_logfiles=TRUE -e websockets_behind_proxy=TRUE -v $DATA_DIR:/data indeXplorer

set DEFAULT_SCALE_X and/or DEFAULT_SCALE_Y to e.g. linear

DEFAULT_SCALE_X=linear
DEFAULT_SCALE_Y=linear

e.g.

docker run --rm -p 80:3838 -e verbose_logfiles=TRUE -e websockets_behind_proxy=TRUE -e DEFAULT_SCALE_X=linear -e DEFAULT_SCALE_Y=linear -v $DATA_DIR:/data indeXplorer