From 2bc2881ad337f38edfec41f2885fbb98a2a0b79a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Sat, 24 Sep 2022 19:36:00 +0100
Subject: [PATCH] docs(readme): update installation instructions
---
README.md | 12 ++++++++----
docs/source/INSTALL.md | 36 ++++++++++++++++++++----------------
2 files changed, 28 insertions(+), 20 deletions(-)
diff --git a/README.md b/README.md
index 01666b16..9d67efde 100644
--- a/README.md
+++ b/README.md
@@ -5,12 +5,12 @@
[](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/pipelines)
[](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/commits/dev)
-The core classes and methods for the python microfluidics, microscopy, data analysis and reporting.
-
-### Installation
-See [INSTALL.md](./INSTALL.md) for installation instructions.
+End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions, post-processing and report production. It leverages the existing Python ecosystem and open-source scientific software available to produce seamless and standardised pipelines.
## Quickstart Documentation
+
+We use (and recommend) [OMERO](https://www.openmicroscopy.org/omero/) to manage our microscopy database, but ALIBY can process both locally-stored experiments and remote ones hosted on a server.
+
### Setting up a server
For testing and development, the easiest way to set up an OMERO server is by
using Docker images.
@@ -38,6 +38,10 @@ To stop them, in the same directory, run:
docker-compose stop
```
+### Installation
+
+See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details.
+
### Raw data access
```python
diff --git a/docs/source/INSTALL.md b/docs/source/INSTALL.md
index 8a46dc42..6aa48b26 100644
--- a/docs/source/INSTALL.md
+++ b/docs/source/INSTALL.md
@@ -1,12 +1,10 @@
# Installation
-Tested on: Mac OSX Mojave and Ubuntu 20.04
-
## Requirements
We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment.
Make sure you are using python 3.
-An environment can be created with using the conda package manager:
+An environment can be created using [Anaconda](https://www.anaconda.com/):
$ conda create --name <env>
$ conda activate <env>
@@ -32,33 +30,39 @@ In your local environment, run:
Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
- $ pyenv install 3.8.13
- $ pyenv virtualenv 3.8.13 aliby
+ $ pyenv install 3.8.14
+ $ pyenv virtualenv 3.8.14 aliby
$ pyenv local aliby
## Pipeline installation
### Pip version
-Once you have created your local environment, run:
+Once you have created and activated your virtual environment, run:
+
+If you are analysing data locally:
+
+ $ pip install aliby
- $ cd aliby
- $ pip install -e ./
+If you are contacting an OMERO server:
+ $ pip install aliby[network]
+
+NOTE: Support for OMERO servers in GNU/Linux computers requires building ZeroC-Ice, thus it requires build tools. The versions for Windows and MacOS are provided as Python wheels and thus installation is faster.
### Git version
We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
-
-In case you want to have local versions (usually for development) the main three aliby dependencies you must install them in a specific order:
+In case you want to have local version:
$ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/aliby.git
- $ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/postprocessor.git
- $ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/agora.git
-
$ cd aliby && poetry install
- $ cd ../postprocessor && poetry install
- $ cd ../agora && poetry install
-And that should install all three main dependencies in an editable mode. The same process can be used for [BABY](https://git.ecdf.ed.ac.uk/swain-lab/aliby/baby)
+This will automatically install the [ BABY ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development.
+
+### Troubleshooting
+
+Segmentation has been tested on: Mac OSX Mojave, Ubuntu 20.04 and Arch Linux.
+Data processing has been tested on all the above and Windows 11.
+
--
GitLab