Merge pull request #236 from benjeffery/example

Update readme and add example.trees

Author: benjeffery

README.md

@@ -1,44 +1,48 @@
 # tsbrowse
-Inspect large genetic genealogies (e.g. ARGs) stored in the [tskit](https://tskit.dev) "succinct tree sequence" format,
-via a genome browser style app. _Tsbrowse_ can deal with ARGs of thousands or potentially millions of samples.
+Inspect large genetic genealogies (e.g. ARGs) stored in the [tskit](https://tskit.dev) "succinct tree sequence" format, via a web app.
+_Tsbrowse_ can scale to ARGs with millions of samples.
+
 It is particularly useful to help evaluate ARGs that have been inferred using tools such as
 [tsinfer](https://github.com/tskit-dev/tsinfer),
 [sc2ts](https://github.com/tskit-dev/sc2ts),
 [Relate](https://github.com/MyersGroup/relate),
 [KwARG](https://github.com/a-ignatieva/kwarg),
 [Threads](https://pypi.org/project/threads-arg/), etc.
 
-To view a tskit tree sequence or tszip file first pre-process it:
+## Quickstart
 
-`python -m tsbrowse preprocess /path/to/trees-file`
+First install `tsbrowse` from PyPI:
+
+`python -m pip install tsbrowse`
+
+A tskit tree sequence must first be preprocessed to a `.tsbrowse` file:
 
-This will write a `.tsbrowse` file
+`python -m tsbrowse preprocess /path/to/trees-file`
 
-To launch the app use:
+This will write a `.tsbrowse` file that can then be viewed using the web app:
 
 `python -m tsbrowse serve /path/to/tsbrowse-file`
 
+This command will launch a web server that can be accessed at `http://localhost:8080` in a web browser.
+
 To display the genes track use:
 
 `python -m tsbrowse serve /path/to/tsbrowse-file --annotations-file genes.`
 
 (where `genes.csv` is a semicolon-separated text file containing no header and information about one gene on a row in the order: `chr;start;end;strand;ensembl ID;gene name`)
 
-To generate a PNG of a specific page use, e.g:
+An example tree sequence file can be found here: [example.trees](https://raw.githubusercontent.com/tskit-dev/tsbrowse/refs/heads/main/example/example.trees.tsz).
 
-`python -m tsbrowse screenshot /path/to/tsbrowse-file mutations`
+## Tips
 
-On WSL, it may be necessary to disable Numba's CUDA support:
+If you are using Windows Subsystem for Linux (WSL) you may need to disable Numba's CUDA support:
 
 `NUMBA_DISABLE_CUDA=1 python -m tsbrowse serve /path/to/tsbrowse-file`
 
-## Installation
+A PNG of a specific page in tsbrowse can be generated using the `screenshot` command:
 
-tsbrowse is currently in development. To install the latest dev version from github, try
+`python -m tsbrowse screenshot /path/to/tsbrowse-file mutations`
 
-```
-python -m pip install git+https://github.com/tskit-dev/tsbrowse
-```
 
 ## Development
 

example/example.trees.tsz

@@ -113,7 +113,10 @@ def preprocess(tszip_path, output, verbose):
 
     preprocess_.preprocess(tszip_path, output, show_progress=True)
     logger.info(f"Preprocessing completed. Output saved to: {output}")
-    print(f"Preprocessing completed. You can now view with `tsbrowse serve {output}`")
+    print(
+        "Preprocessing completed. You can now view with "
+        f"`python -m tsbrowse serve {output}`"
+    )
 
 
 @cli.command()