Fixes

README.md

@@ -30,12 +30,11 @@ Useful links:
 
 
 We recommend installing immuneML inside a virtual environment.
-immuneML uses Python 3.8 or later. If using immuneML simulation, Python 3.11 or later is recommended.
-
+immuneML uses **Python 3.9 or later**. If using immuneML simulation, Python 3.11 or later is recommended.
 immuneML can be [installed directly using a package manager](<https://docs.immuneml.uio.no/latest/installation/install_with_package_manager.html#>) such as pip or conda,
 or [set up via docker](<https://docs.immuneml.uio.no/latest/installation/installation_docker.html>).
 
-Quick installation:
+#### Quick installation (immuneML essentials):
 
 ```bash
 python3 -m venv ./immuneml_venv/
@@ -47,11 +46,13 @@ pip install immune-ml
 or
 
 ```bash
-conda create --prefix immuneml_env/ python=3.8
+conda create --prefix immuneml_env/ python=3.11
 conda activate immuneml_env/
 conda install -c bioconda immuneml
 ```
 
+#### Detailed installation (immuneML extras):
+
 Please check the documentation for more detailed instructions or [how to install optional dependencies](<https://docs.immuneml.uio.no/latest/installation/install_with_package_manager.html#installing-optional-dependencies>).
 
 ### Validating the installation

docs/source/developer_docs/install_for_development.rst

@@ -16,7 +16,7 @@ Prerequisites
 
 - System requirements: at least 4GB of RAM memory and 15GB of disk space.
 
-- A Python virtual environment using at least Python version 3.8 (newest version of Python is usually recommended). This can be created through `Python venv <https://docs.python.org/3/library/venv.html>`_ or `conda venv <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
+- A Python virtual environment using **at least Python version 3.9** (newest version of Python is usually recommended). This can be created through `Python venv <https://docs.python.org/3/library/venv.html>`_ or `conda venv <https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_.
 
 - Under Windows, the Microsoft Visual C++ 14.0 or greater is required to install from requirements.txt.
 

docs/source/galaxy.rst

@@ -10,37 +10,18 @@ immuneML & Galaxy
    :twitter:image: https://docs.immuneml.uio.no/_images/receptor_classification_overview.png
 
 
-All of immuneMLs functionalities are also available through `a Galaxy web interface <https://galaxy.immuneml.uiocloud.no>`_ as a collection of Galaxy tools. We provide a YAML-based Galaxy
-tool that is equivalent to the CLI (command-line interface), as well as repertoire and receptor-level classification tools with an intuitive
-graphical user interface aimed at immunology experts without a machine learning background.
-
+All of immuneMLs functionalities are also available through `a Galaxy web interface <https://avant.immuneml.uiocloud.no>`_ as a collection of Galaxy tools.
+The immuneML Galaxy tools provide simplified, button-based interfaces to get started running different types of immuneML analyses,
+or can alternatively be run with a YAML input file to specify all parameters.
 
 .. toctree::
   :maxdepth: 1
-  :caption: Galaxy tutorial
+  :caption: Galaxy tutorials
 
   galaxy/galaxy_intro
+  galaxy/galaxy_tools
+  galaxy/galaxy_immunologist_friendly
 
-.. toctree::
-  :maxdepth: 1
-  :caption: Galaxy dataset tutorials:
-
-  galaxy/galaxy_dataset
-  galaxy/galaxy_import_remote_data
-  galaxy/galaxy_simulate_dataset
-  galaxy/galaxy_simulate_signals
-
-.. toctree::
-  :maxdepth: 1
-  :caption: Galaxy simple analysis tutorials:
-
-  galaxy/galaxy_simple_receptors
-  galaxy/galaxy_simple_repertoires
-
-.. toctree::
-  :maxdepth: 1
-  :caption: Galaxy advanced analysis tutorials:
-
-  galaxy/galaxy_train_ml_models
-  galaxy/galaxy_general_yaml
+..
+   _Note: galaxy_import_remote_data is currently not linked in the docs, should be linked once those tools are made available on new galaxy server