Update singularity docs

docs/docker_and_singularity.md

@@ -1,56 +1,38 @@
 # Docker and Singularity
 
 This are the steps to create a Singularity Image File (SIF) for oplab_pipeline.
+There exists a Dockerfile as well, but it's recommended to use the SIF image
+instead.
 
-## 1. Build the docker image. 
-This assumes that you have installed Docker previously. If you haven't, follow [these installation instructions for Docker](https://docs.docker.com/get-docker/). At the root of oplab_pipeline, run
+## 1. Build the Singularity image. 
+This assumes you have installed Singularity previously. If you havent, follow [these installation instructions for Singularity.](https://sylabs.io/guides/master/user-guide/quick_start.html#quick-installation-steps)
 
-```
-docker build --tag oceanperception/oplab_pipeline .
+```sh
+sudo singularity build oplab_pipeline.sif oplab_pipeline.def
 ```
 
-Check that your image works correcty by running `auv_nav` help using the following command:
+# 3. Run the SIF image.
+The previous instruction will have saved a file `oplab_pipeline.sif` in this same directory. This is your containerised image file. You can use this SIF file in any Linux computer with Singularity installed. To see the help, run
 
 ```sh
-docker run -it oceanperception/oplab_pipeline auv_nav -h
+singularity run oplab_pipeline.sif
 ```
 
-this command should return the following output (as per version 0.1.10):
+Run the pipeline using the following command:
+ - `singularity exec oplab_pipeline.sif auv_nav ARGS`
+ - `singularity exec oplab_pipeline.sif auv_cal ARGS`
+ - `singularity exec oplab_pipeline.sif correct_images ARGS`
 
-```
-     ● ●  Ocean Perception
-     ● ▲  University of Southampton
-
- Copyright (C) 2020 University of Southampton
- This program comes with ABSOLUTELY NO WARRANTY.
- This is free software, and you are welcome to
- redistribute it.
-
-INFO ▸ Running auv_nav version unknown-commit
-usage: auv_nav [-h] {parse,process,convert} ...
-
-positional arguments:
-  {parse,process,convert}
-    parse               Parse raw data and converting it to an intermediate dataformat for further processing. Type
-                        auv_nav parse -h for help on this target.
-    process             Process and/or convert data. Data needs to be saved in the intermediate data format generated
-                        using auv_nav.py parse. Type auv_nav process -h for help on this target.
-    convert             Converts data.
-
-optional arguments:
-  -h, --help            show this help message and exit
-```
+## FAQ
 
-# 2. Convert the docker image to SIF. 
-This assumes you have installed Singularity previously. If you havent, follow [these installation instructions for Singularity.](https://sylabs.io/guides/master/user-guide/quick_start.html#quick-installation-steps)
+If you see the following error:
 
 ```sh
-singularity build oplab_pipeline.sif docker-daemon://oceanperception/oplab_pipeline:latest
+/opt/oplab_pipeline_env/lib/python3.9/site-packages/joblib/_multiprocessing_helpers.py:45: UserWarning: [Errno 2] No such file or directory.  joblib will operate in serial mode
+  warnings.warn('%s.  joblib will operate in serial mode' % (e,))
 ```
 
-# 3. Run the SIF image.
-The previous instruction will have saved a file `oplab_pipeline.sif` in this same directory. This is your containerised image file. You can use this SIF file in any Linux computer with Singularity installed. To use it, run
-
-```sh
-singularity run oplab_pipeline.sif auv_nav -h
-```
+run the SIF image with the flag `-B /run/shm:/run/shm` Example:
+- `singularity exec -B /run/shm:/run/shm oplab_pipeline.sif auv_nav ARGS`
+- `singularity exec -B /run/shm:/run/shm oplab_pipeline.sif auv_cal ARGS`
+- `singularity exec -B /run/shm:/run/shm oplab_pipeline.sif correct_images ARGS`