Update README.md

README.md

@@ -1,41 +1,56 @@
 # METIS Pipeline
 METIS pipe line is the data reduction software for ELT early science instrument of Mid-IR imager and spectrograph.
 
+## Manual Installation
+
+See the `README.md` in the `metisp` directory for manual installation of the pipeline.
+
 ## Installation via Docker
 
 Follow the installation instructions for [Docker Engine](https://docs.docker.com/engine/install/)
 
 
 Clone the git repo
 
-> git clone https://github.com/AstarVienna/METIS_Pipeline.git
+```
+git clone https://github.com/AstarVienna/METIS_Pipeline.git
+```
 
 Build the image
 
-> docker build -t metispipeline .
+```
+docker build -t metispipeline .
+```
 
 Run the image
 
-
-> docker run -ti --net=host --env="DISPLAY" --volume="\$HOME/.Xauthority:/home/metis/.Xauthority:rw" --mount type=bind,source="\$(pwd)",target=/home/metis/METIS_Pipeline metispipeline
+```
+docker run -ti --net=host --env="DISPLAY" --volume="$HOME/.Xauthority:/home/metis/.Xauthority:rw" --mount type=bind,source="$(pwd)",target=/home/metis/METIS_Pipeline metispipeline
+```
 
 
 List all images and containers
 
-> docker image list
-> docker container list
+```
+docker image list
+docker container list
+```
 
 Delete image or container
 
-> docker container rm \<nameofcontainer\>
-> docker image rm metispipeline
+```
+docker container rm <nameofcontainer>
+docker image rm metispipeline
+```
 
 ## Running the pipeline
 
 While inside the docker image
 
-> pyesorex --recipes 
-> pyesorex metis_det_lingain "\${SOF_DIR}/metis_lm_lingain.sof"
-> edps -w metis.metis_lm_img_wkf -i \$SOF_DATA -c
-> edps -w metis.metis_lm_img_wkf -i \$SOF_DATA
+```
+pyesorex --recipes 
+pyesorex metis_det_lingain "${SOF_DIR}/metis_lm_lingain.sof"
+edps -w metis.metis_lm_img_wkf -i $SOF_DATA -c
+edps -w metis.metis_lm_img_wkf -i $SOF_DATA
+```