Add makoview information to the docs

Author: olliecheng

getting-started.md

@@ -56,3 +56,19 @@ Configuration settings can be found in [Configuration](configuration).
 
 {: .note }
 If your institution has an [nf-core configuration](https://nf-co.re/configs/) available, you can access it through `-profile` i.e. `-profile wehi` to use the WEHI Milton HPC. See [Execution Profiles](deployment#execution-profiles) for more.
+
+## Running makoview
+
+Once the pipeline has finished, you can run the visualisation tool `makoview` using:
+
+```bash
+export MAKO_OUTPUT_DIR="/data/gpfs/projects/punim0614/occheng/epi_differential/pipeline/runs/longbench/results"
+export MODCALLER="dorado"  # either "dorado" or "m6anet"
+export DIFFERENTIAL_MODEL="adaptive_binomial"
+uvx makoview \
+  --differential-results $MAKO_OUTPUT_DIR/differential/$MODCALLER/${DIFFERENTIAL_MODEL}_fits.tsv \
+  --modification-db $MAKO_OUTPUT_DIR/modcall/$MODCALLER/all_sites.duckdb \
+  --port 8000
+```
+
+See [makoview](makoview) for more information on alternative installation methods for Makoview and remote forwarding.

makoview.md

@@ -0,0 +1,67 @@
+---
+title: makoview
+layout: default
+nav_order: 6
+---
+
+Mako comes with an interactive application called **_makoview_** which can be used to visualise the results once the pipeline has finished.
+
+## Installation
+
+makoview is a Python package for Python 3.9 — 3.12.12, available on PyPI and downloadable through your preferred Python package manager.
+
+```bash
+# with pip:
+$ pip install makoview
+$ makoview --help
+
+# with pipx:
+$ pipx run makoview --help
+
+# using uvx (✅ recommended!!)
+$ uvx makoview --help        # or uvx --python 3.12 makoview --help
+```
+
+[`pipx`](https://github.com/pypa/pipx) and [`uv`](https://docs.astral.sh/uv/) allow executables to be run within their own isolated environment, preventing dependency resolution issues. They are recommended over `pip install`.
+
+## Usage
+
+Makoview has three parameters:
+
+```bash
+options:
+  -h, --help            show this help message and exit
+  --differential-results DIFFERENTIAL_RESULTS
+                        Path to differential sites database file
+  --modification-db MODIFICATION_DB
+                        Path to modification database file
+  --port PORT           Port for the Shiny application (default: 8000)
+```
+
+The default usage is as follows:
+
+```bash
+export MAKO_OUTPUT_DIR="/data/gpfs/projects/punim0614/occheng/epi_differential/pipeline/runs/longbench/results"
+export MODCALLER="dorado"  # either "dorado" or "m6anet"
+export DIFFERENTIAL_MODEL="adaptive_binomial"
+makoview \
+  --differential-results $MAKO_OUTPUT_DIR/differential/$MODCALLER/${DIFFERENTIAL_MODEL}_fits.tsv \
+  --modification-db $MAKO_OUTPUT_DIR/modcall/$MODCALLER/all_sites.duckdb \
+  --port 8000
+```
+
+This will launch a web server running on port `8000`, accessible at [http://127.0.0.1:8000](http://127.0.0.1:8000).
+
+### Running on HPC
+
+On HPC systems, if you have SSH access, you can port forward the web server from the server to your local machine.
+
+```bash
+# launch the server on port within [10000, 65535], i.e.
+🛜 SERVER $ makoview <params> --port <abcde>
+
+# next, on your local machine, forward that port:
+👩‍💻 CLIENT $ ssh -L <abcde>:localhost:<abcde> username@hpc.server
+```
+
+You can now connect to Makoview locally using `http://127.0.0.1:<abcde>`.