From 1037dbb6944cf5f90dc2c5bb7318df0f51f171a3 Mon Sep 17 00:00:00 2001
From: Xavier Robin <xavier.robin@unibas.ch>
Date: Wed, 28 May 2025 09:45:36 +0200
Subject: [PATCH] doc: clarify conda setup

---
 README.md                  | 34 ++++++++++++++++++++++++----------
 examples/scoring/README.md |  6 ++++--
 2 files changed, 28 insertions(+), 12 deletions(-)

diff --git a/README.md b/README.md
index 87fe83e9..a4cf05de 100644
--- a/README.md
+++ b/README.md
@@ -15,24 +15,37 @@ Please do not hesitate to contact us for feedback or troubleshooting:
 
 ## OpenStructure Installation
 
-For a simple and portable setup, we recommend using a conda or a containerized
-solution. OpenStructure provides its own Docker container registry,
-making deployment easier. Deploying a docker image just needs a
-docker pull which typically finishes in about a minute depending
-on your local hardware and internet connection. Singularity
-containers bootstrap from the docker container but must be built
-by the user. 
-
 ### Conda
 
+OpenStructure is available as a [conda package on
+Bioconda](https://bioconda.github.io/recipes/openstructure/README.html) for a simple and portable setup.
+You can install it with the following command:
+
 ```
 conda install bioconda::openstructure
 ```
 
 Tested with [miniforge](https://conda-forge.org/miniforge/).
 
+You can then run a test script:
+
+```
+wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
+ost test_ost.py
+```
+
+### Containers
+
+For a fully portable setup, we provide containerized solutions.
+OpenStructure provides its own Docker container registry,
+making deployment easier. Deploying a docker image just needs a
+docker pull which typically finishes in about a minute depending
+on your local hardware and internet connection. Singularity
+containers bootstrap from the docker container but must be built
+by the user. Both solutions require root permissions.
 
-### Docker
+
+#### Docker
 
 For complete documentation on using Docker with OpenStructure, 
 [click here](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/docker).
@@ -51,7 +64,8 @@ And run a test script:
 wget https://git.scicore.unibas.ch/schwede/openstructure/-/raw/master/docker/test_docker.py -O test_ost.py
 docker run --rm -v $(pwd):/home registry.scicore.unibas.ch/schwede/openstructure:latest test_ost.py
 ```
-### Singularity
+
+#### Singularity
 
 For complete documentation on using Singularity with OpenStructure, 
 [click here](https://git.scicore.unibas.ch/schwede/openstructure/tree/master/singularity).
diff --git a/examples/scoring/README.md b/examples/scoring/README.md
index eeb64eed..a75c98cf 100644
--- a/examples/scoring/README.md
+++ b/examples/scoring/README.md
@@ -20,8 +20,8 @@ unzip -j example.zip
 
 The example commands here assume an OpenStructure installation
 ([compile instructions](https://openstructure.org/docs/install/)).
-Running the computations in conda or containers provide a considerably easier
-setup than compiling OpenStructure from source. Instructions for setup and
+To simplify the setup, we recommend Conda or containers instead of compiling
+OpenStructure from source. Instructions for setup and
 running equivalent computations are available below for
 
 * [Conda](#conda)
@@ -90,6 +90,8 @@ PDB format, ligands must be provided in SDF format.
 
 # Conda
 
+OpenStructure is available as a [conda package on
+Bioconda](https://bioconda.github.io/recipes/openstructure/README.html)
 Installing OpenStructure in Conda is as easy as:
 
 ```
-- 
GitLab