Skip to content
Snippets Groups Projects
Commit b7267929 authored by Arnaud Duvermy's avatar Arnaud Duvermy
Browse files

update readme

Former-commit-id: cd2306ba317786dde505eb98999de8a07c42814e
Former-commit-id: 7bdcf10b634eef9e54de471d484d59811a67033a
Former-commit-id: 806b92364c38f2ed0b5a34c1572995131228b0ca
parent 56f398bd
No related branches found
No related tags found
No related merge requests found
......@@ -69,35 +69,6 @@ docker pull ruanad/htrfit:v2.0.0
docker run -it --rm ruanad/htrfit:v2.0.0
```
HTRfit allows building graphs to visualize results. Inside Docker, displaying a window from the R terminal can be tricky and requires specific settings before running the container. Following commands worked for us:
```sh
# Prepare target env
CONTAINER_DISPLAY="0"
CONTAINER_HOSTNAME="htrfit_user"
# Create a directory for the socket
mkdir -p display/socket
touch display/Xauthority
# Get the DISPLAY slot
DISPLAY_NUMBER=$(echo $DISPLAY | cut -d. -f1 | cut -d: -f2)
# Extract current authentication cookie
AUTH_COOKIE=$(xauth list | grep "^$(hostname)/unix:${DISPLAY_NUMBER} " | awk '{print $3}')
# Create the new X Authority file
xauth -f display/Xauthority add ${CONTAINER_HOSTNAME}/unix:${CONTAINER_DISPLAY} MIT-MAGIC-COOKIE-1 ${AUTH_COOKIE}
# Proxy with the :0 DISPLAY
socat UNIX-LISTEN:display/socket/X${CONTAINER_DISPLAY},fork TCP4:localhost:60${DISPLAY_NUMBER} &
# Launch the container
docker run -it --rm \
-e DISPLAY=:${CONTAINER_DISPLAY} \
-e XAUTHORITY=/tmp/.Xauthority \
-v ${PWD}/display/socket:/tmp/.X11-unix \
-v ${PWD}/display/Xauthority:/tmp/.Xauthority \
--hostname ${CONTAINER_HOSTNAME} \
ruanad/htrfit:v2.0.0-beta
## inspired by : https://blog.yadutaf.fr/2017/09/10/running-a-graphical-app-in-a-docker-container-on-a-remote-server/
```
## Biosphere virtual machine
A straightforward way to use **HTRfit** is to run it on a Virtual Machine (VM) through [Biosphere](https://biosphere.france-bioinformatique.fr/catalogue/). We recommend utilizing a VM that includes RStudio for an integrated development environment (IDE) experience. Biosphere VM resources can also be scaled according to your simulation needs.
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment