Commit cc43bfcb authored by Michele Compostella's avatar Michele Compostella
Browse files

Updated readme

parent 2d9b8b1b
......@@ -39,7 +39,7 @@ ENV DEBIAN_FRONTEND noninteractive
ENV QUIP_ARCH linux_x86_64_gfortran
ENV QUIP_STRUCTS_DIR $PREFIX/QUIP/structs
ENV QUIP_INSTALLDIR $PREFIX/QUIP/bin
USER root
USER $USER
WORKDIR /root/
# Updating distro
......
......@@ -29,12 +29,19 @@ The workflow presented in this repository uses the GAP library for the software
## Installation
Clone this repository to your local machine with
```shell
git clone https://gitlab.mpcdf.mpg.de/mcompo/favad.git
```
After cloning this repository, run the following command to create the Docker image
```shell
cd favad
./build.sh /root/software/
```
Note that building the Docker image requires root permission on the local machine.
The parameter for the build.sh script is the installation path of the software stack inside the Docker image.
Additional optional parameters can be provided to automatically accept the GAP license agreement:
......@@ -46,11 +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, use the following command to shell into the container:
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:
```shell
docker run -t -i --volume /local_folder/:/root/sample/output/ favad /bin/bash
docker run -t -i --volume $HOME/favad_output/:/root/sample/output/ favad /bin/bash
```
The ouput files generated inside the Docker container will be stored in the specified /local_folder/.
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.
At this point you can run the workflow for fingerprinting and visualizing defects on the sample dataset inside the Docker container:
......@@ -76,7 +85,7 @@ By running the installer, you are accepting the [GAP license agreement](http://w
If you installed the software stack locally, you can run the workflow for fingerprinting and visualizing defects on the sample dataset using
```shell
cd ./sample
python3 FaVa.py -p ./parameters.txt
python3 FaVaD.py -p ./parameters.txt
```
Note however that you are required to change the paths in the parameter.txt file to match the current location of the files and software executables.
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