Simplify documentation

docs/src/installation.md

@@ -2,132 +2,15 @@
 This project is developed using [Julia](https://julialang.org/).
 For ease of use and to maximize reproducibility we also provide container images using Singularity.
 
-This project was developed on Linux, and deployed on scientific computing clusters running Linux. The Singularity workflow ensures both local and cluster computations run **exactly** the same. The automated tests run the exact same environment.
+The fastest and easiest way is to clone the repository using [Git](https://git-scm.com/). Alternatively you can download zipped [releases](https://github.com/bencardoen/SubPrecisionContactDetection.jl/archive/refs/heads/main.zip).
+The below assumes you have Julia 1.9 or higher installed.
 
-This cannot be guaranteed across different OS'es (e.g. Windows, MacOs). While there are no technical reasons preventing the code from working on any OS, you may run into issues as it is not something we actively use ourselves.
-
-<a name="singularity"></a>
-### Portable & fastest way using Singularity
-You can use an optimized [Singularity](https://docs.sylabs.io/guides/2.6/user-guide/installation.html#) image, which has all dependencies pre-installed.
-
-If you do not have Singularity, please see the documentation for detailed [installation instructions](https://docs.sylabs.io/guides/2.6/user-guide/installation.html#).
-
-The below steps are examples, but may not be complete for each platform, for the reference instructions, please visit [installation instructions](https://docs.sylabs.io/guides/2.6/user-guide/installation.html#).
-
-#### Singularity on Linux
-Fedora/RPM
-```bash
-sudo dnf install singularity
-```
-
-#### Singularity on Windows
-To run Singularity on Windows, set up [WSL2](https://www.blopig.com/blog/2021/09/using-singularity-on-windows-with-wsl2/) or refer to [installation instructions](https://docs.sylabs.io/guides/2.6/user-guide/installation.html#).
-
-#### Singularity on MacOS
-See [instructions](https://docs.sylabs.io/guides/2.6/user-guide/installation.html#install-on-mac).
-
-#### Download the image
-
-Download the [image](http://vault.sfu.ca/index.php/s/QJ4Evcet4oVWXPL/download) as *mcsdetect.sif*.
-For example, using wget (Linux), you could do:
-```bash
-wget -O mcsdetect.sif http://vault.sfu.ca/index.php/s/QJ4Evcet4oVWXPL/download
-```
-
-On MacOS you can install wget using:
-```bash
-brew install wget
-```
-
-### Using the image
-First, make sure execute permissions are set:
-```bash
-chmod u+x mcsdetect.sif
-```
-
-#### Starting an interactive Julia session
-```bash
-./mcsdetect.sif
-```
-Expected output:
-
-![](./assets/julia.png)
-
-#### Running code snippets
-```bash
-chmod u+x mcsdetect.sif
-./mcsdetect.sif -e 'using SubPrecisionContactDetection;'
-```
-Expected output:
-
-![](./assets/snippet.png)
-
-#### Running the analysis scripts
+In an empty, new folder:
 ```bash
-chmod u+x mcsdetect.sif
-./mcsdetect.sif /opt/SubPrecisionContactDetection.jl/scripts/ercontacts.jl ARGS
-```
-Where you'd replace ARGS with arguments to the script as documented in [scripts/ercontacts.jl](https://github.com/bencardoen/SubPrecisionContactDetection.jl/blob/main/scripts/ercontacts.jl).
-Run it without arguments to get the help prompt.
-
-Expected output:
-![](./assets/ercontact.png)
-
-<a name="julia"></a>
-### Install as a Julia package
-
-**Note due to a [bug with conda](https://github.com/conda/conda/issues/10111) MacOS installations will have some tests failing, the module itself is functional**
-
-You can either add to the global Julia installation:
-
-```bash
-julia -e 'using Pkg;Pkg.add(url="https://github.com/bencardoen/Colocalization.jl.git");Pkg.add(url="https://github.com/bencardoen/ERGO.jl.git");Pkg.add(url="https://github.com/bencardoen/SPECHT.jl.git");Pkg.add(url="https://github.com/bencardoen/SubPrecisionContactDetection.jl.git")'
-julia -e 'using Pkg; Pkg.build("SubPrecisionContactDetection");Pkg.test("SubPrecisionContactDetection")'
-```
-
-
-Or create a new environment and install it there:
-
-```bash
-mkdir -p test
-cd test
-julia --project=. -e 'using Pkg;Pkg.add(url="https://github.com/bencardoen/Colocalization.jl.git);Pkg.add(url="https://github.com/bencardoen/ERGO.jl.git");Pkg.add(url="https://github.com/bencardoen/SPECHT.jl.git");Pkg.add(url="https://github.com/bencardoen/SubPrecisionContactDetection.jl.git")'
-julia --project=. -e 'using Pkg; Pkg.build("SubPrecisionContactDetection");Pkg.test("SubPrecisionContactDetection")'
-```
-
-In both cases, you should see that all tests pass:
-
-![](./assets/pass.png)
-
-### Install the cloned repository (gives access to the processing CLI interface)
-```bash
-git clone https://github.com/bencardoen/SubPrecisionContactDetection.jl.git
+git clone https://github.com/bcardoen/SubPrecisionContactDetection.jl.git
 cd SubPrecisionContactDetection.jl
-julia --project=. installlocal.jl
-```
-
-This should result in output similar to this screenshot:
-
-![](./assets/clone.png)
-
-
-<a name="windows"></a>
-### 1.3 Windows
-- Install [VSCode](https://code.visualstudio.com/download)
-- Install [Python](https://www.python.org/downloads/)
-- Install [Julia 1.9](https://julialang-s3.julialang.org/bin/winnt/x64/1.9/julia-1.9.4-win64.exe)
-In VSCode, create a new folder and open VSCode inside of it.
-
-Then:
-- New Terminal
-In the terminal, type:
-```bash
-git clone https://github.com/bencardoen/SubPrecisionContactDetection.jl.git
-```
-This will download the latest version of the source code.
-**Note** Python needs to be installed and defined, make sure of this step before proceeding.
-Now we will build it:
-```
-julia --project=. -e 'using Pkg; Pkg.build() Pkg.test()'
+julia --project=. -e `using Pkg; Pkg.build(); Pkg.test()`
 ```
+This downloads the source code in a subfolder, builds it with all dependencies and tests it.
 
+Once you have this, you can use either a terminal or an IDE (e.g. Visual Studio Code) to work with the source code to process new datasets.