Commit b118a61b authored by Michele Compostella's avatar Michele Compostella
Browse files

Removing choice for installation directory in the container

parent cc43bfcb
......@@ -53,14 +53,13 @@ If these optional parameters are not specified, the build process will ask for t
## How to run the Docker image
Once the Docker image has been created and the [Docker daemon is running](https://docs.docker.com/config/daemon/), you can shell into the container mounting a local folder where the output is stored using:
Once the Docker image has been created and the [Docker daemon is running](https://docs.docker.com/config/daemon/), you can shell into the container mounting a local folder where the output files will be stored, using:
```shell
docker run -t -i --volume $HOME/favad_output/:/root/sample/output/ favad /bin/bash
sudo docker run -t -i --volume $HOME/favad_output/:/root/sample/output/ favad /bin/bash
```
Using the previous command, the ouput files generated inside the Docker container will be stored in $HOME/faved_output/.
Please note that the content of this folder will be overwritten, if the folder is not empty.
Using the previous command, the ouput files generated inside the Docker container will be available in $HOME/faved_output/ of your local machine. Please note that the content of this folder will be overwritten, if the folder is not empty.
At this point you can run the workflow for fingerprinting and visualizing defects on the sample dataset inside the Docker container:
```shell
......
......@@ -27,11 +27,11 @@
## This software provides a workflow for fingerprinting and visualizing defects in damaged crystal
## structures. The theoretical background is presented in: paper_ID
##
## Run as root with:
## ./build.sh /installation_path/ "I agree" full_name email_address organization
## Run with:
## ./build.sh "I agree" full_name email_address organization
##
## For example:
## ./build.sh /home/aurelius/software/ "I agree" "Marcus Aurelius" marcus.aurelius@email.com "Imperium Romanum"
## ./build.sh "I agree" "Marcus Aurelius" marcus.aurelius@email.com "Imperium Romanum"
##
###############################################################################################################
......@@ -39,22 +39,13 @@
set -e
set -o pipefail
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
trap 'echo "\"${last_command}\" command filed with exit code $?."' EXIT
trap 'echo "\"${last_command}\" command failed with exit code $?."; echo; echo "Build process interrupted!"; echo' EXIT
# Reading input parameters
PREFIX=$1
GAP=$2
NAME=$3
EMAIL=$4
ORGANIZATION=$5
# Requiring at least the PREFIX parameter
if [ "$#" -lt 1 ]; then
echo
echo "Please provide the installation directory for the software in the Docker container"
echo "E.g: ./build.sh /root/software/"
exit
fi
GAP=$1
NAME=$2
EMAIL=$3
ORGANIZATION=$4
# GAP license
if [ ! -f ./software/GAP.tar.gz ] && [ "$GAP" != "I accept" ]; then
......@@ -68,6 +59,7 @@ if [ ! -f ./software/GAP.tar.gz ] && [ "$GAP" != "I accept" ]; then
read GAP
if [ "$GAP" != "I accept" ]; then
echo "You did not accept the GAP license. Leaving installation process.."
trap - EXIT
exit
fi
echo "Enter your name for the GAP license"
......@@ -87,6 +79,7 @@ fi
if [ ! -f ./software/kdtree2.tar.gz ]; then
echo
echo "kdtree2.tar.gz archive is missing from the ./software/ folder. Leaving installation.."
trap - EXIT
exit
fi
......@@ -120,13 +113,13 @@ echo
echo "Build complete!"
echo
echo "You can run the image interactively mounting an ouput folder (use the full path) with:"
echo " sudo docker run -t -i --volume /local_folder/:/root/sample/output/ favad /bin/bash"
echo " sudo docker run -t -i --volume $HOME/favad_output/:/root/sample/output/ favad /bin/bash"
echo "and, once in the container"
echo " cd /root/sample/"
echo " python3 FaVaD.py -p /root/sample/parameters.txt"
echo
# Disarming trap and exit
trap - EXIT
exit 0
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment