Solved issues regarding Docker Setup

Resolved some issues with the Docker setup. Specifically, the problem was that the relative path of the INSTALL directory was specified in the Makefile. However, Docker requires absolute paths, which caused the UPSET not to be found. Additionally, in the updated version, the overall data folder is provided in the Docker container, allowing the user to save reports, etc., and to open or edit them on the native machine.

Also, updated the instructions regarding the Docker setup, both in the README file and the documentation as well.

Co-Authored-By: D.Vali <[email protected]>
Co-Authored-By: zazatisn <[email protected]>

Author: 3 people

Docker_files/create_docker/Makefile

@@ -1,15 +1,15 @@
 TAG=asp_docker_ubuntu
 VERSION=v1
 IMAGE=upset_docker_ubuntu
-UPSET_PATH=../data/INSTALL
+DATADIR := $(abspath $(dir $(lastword $(MAKEFILE_LIST)))/../data)
 
 build-docker:
 	-docker image rm -f $(IMAGE):$(VERSION)
 	docker build -t  $(IMAGE):$(VERSION) .
 
 run:
 	-docker container rm $(TAG) -f
-	docker run -it  --security-opt label=type:container_runtime_t --network=host -e DISPLAY=$$DISPL -v ${UPSET_PATH}:/home/UPSET -v /tmp/.X11-unix:/tmp/.X11-unix --name $(TAG) $(IMAGE):$(VERSION)
+	docker run -it  --security-opt label=type:container_runtime_t --network=host -e DISPLAY=$$DISPLAY -v -v $(DATADIR)/:/home/data -v /tmp/.X11-unix:/tmp/.X11-unix --name $(TAG) $(IMAGE):$(VERSION)
 
 sh:
 	docker exec -it $(TAG) /bin/bash

Docker_files/use_docker/Makefile

@@ -1,15 +1,15 @@
 TAG=asp_docker_ubuntu
 VERSION=v1
 IMAGE=upset_docker_ubuntu
-UPSET_PATH=../data/INSTALL
+DATADIR := $(abspath $(dir $(lastword $(MAKEFILE_LIST)))/../data)
 
 build-docker:
 	-docker image rm -f $(IMAGE):$(VERSION)
 	docker build -t  $(IMAGE):$(VERSION) .
 
 run:
 	-docker container rm $(TAG) -f
-	docker run -it  --security-opt label=type:container_runtime_t --network=host -e DISPLAY=$$DISPL -v ${UPSET_PATH}:/home/UPSET -v /tmp/.X11-unix:/tmp/.X11-unix --name $(TAG) $(IMAGE):$(VERSION)
+	docker run -it  --security-opt label=type:container_runtime_t --network=host -e DISPLAY=$$DISPLAY -v -v $(DATADIR)/:/home/data -v /tmp/.X11-unix:/tmp/.X11-unix --name $(TAG) $(IMAGE):$(VERSION)
 
 sh:
 	docker exec -it $(TAG) /bin/bash

README.md

@@ -45,15 +45,22 @@ In order to run UPSET with docker, the user needs to download the UPSET tarball
 
 ```bash
 cd Docker_files
+# Create the data folder and copy the INSTALL folder inside it
 mkdir data
-cp -r <INSTALL folder> data
-cd create_docker
+cd data
+cp -r <INSTALL folder> ./
+# Build the docker image
+cd ../create_docker
 make build-docker
+# Run the docker container
 cd ../use_docker
+xhost +
 make run
 
 /* In Docker Environment */
-cd /home/UPSET
+cd /home/data/UPSET
+export UPSET_INSTALL_DIR = $PWD
+./UPSET-setup.sh
 ./UPSET
 
 /* Save/Load Docker Image */
@@ -63,6 +70,8 @@ cd use_docker
 make load
 ```
 
+More information regarding the use of UPSET in a docker container can be found [here](https://circuits-and-systems-lab-caslab.github.io/UPSET/docker_setup/).
+
 ## DEMO
 Below there is a demo video of perfoming an exhaustive SET analysis in UPSET.
 

docs/docker_setup.md

@@ -24,6 +24,7 @@ This section explains the used docker filesystem while also act as a guide on ho
 ## Build Docker Image
 | Command | Description |
 | --- | --- |
+| `> cd Docker_files` | Go to Docker_files folder of UPSET repository |
 | `> mkdir data` | Create the data folder |
 | `> cd data` | Go to data folder |
 | `> cp -r <INSTALL folder> ./` | Copy the desired INSTALL folder |
@@ -42,6 +43,7 @@ This section explains the used docker filesystem while also act as a guide on ho
 | Command | Description |
 | --- | --- |
 | `> cd ../use_docker` | Go to use_docker folder |
+| `> xhost +` | Ensure that you can open UPSET GUI insde the docker container |
 | `> make run` | Run the docker container |
 | `> make sh` | Run in different terminal if container is already running without terminating it [optional] |
 
@@ -50,10 +52,22 @@ This section explains the used docker filesystem while also act as a guide on ho
     If you want to run on different terminal then use `make sh`.
     Also, running `make sh` without prior `make run` will not work.
 
-
 ## Docker/VM Filesystem
 | Folder | Description |
 | --- | --- |
 | `/home` | Home |
 | `/home/data/<INSTALL folder>` | UPSET folder |
-| `/home/data` | Data (Shared) Folder |
+| `/home/data` | Data (Shared) Folder |
+
+# Run UPSET in Docker
+
+After building the docker image and running the docker container, you can run UPSET in the docker container.
+
+## Run UPSET
+
+| Command | Description |
+| --- | --- |
+| `> cd /home/data/UPSET` | Go to UPSET folder |
+| `> export UPSET_INSTALL_DIR = $PWD` | Set the UPSET_INSTALL_DIR environment variable |
+| `> ./UPSET-setup.sh` | Run the setup script |
+| `> ./UPSET` | Run UPSET |