update readme

README.md

@@ -7,6 +7,18 @@
 ![Pylint](https://medema-group.github.io/BiG-SCAPE/badges/pylint.svg)
 
 
+# BiG-SCAPE
+
+**BiG-SCAPE** (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.
+
+As input, BiG-SCAPE takes GenBank files from the output of [antiSMASH](https://antismash.secondarymetabolites.org) with BGC predictions, as well as reference BGCs from the [MIBiG repository](https://mibig.secondarymetabolites.org/). As output, BiG-SCAPE generates tab-delimited output files, as well as a rich HTML visualization.
+
+In principle, BiG-SCAPE can also be used on any other gene clusters, such as pathogenicity islands, secretion system-encoding gene clusters, or even whole viral genomes.
+
+If you find BiG-SCAPE useful, please [cite us]() [TODO V2].
+
+
+
 ## Running BiG-SCAPE
 
 There are a few ways to run BiG-SCAPE, depending on your needs.
@@ -18,26 +30,16 @@ Software:
 - python 3.11 or up
 - conda/mamba
 
-All steps start with cloning the repository:
-
-`git clone https://github.com/medema-group/BiG-SCAPE`.
-
-All other steps assume you are in the BiG-SCAPE directory, using cd `BiG-SCAPE`.
-
-The most straightforward ways of installing are using Docker or Hatch.
-However, these do not allow you to run the application from anywhere using a command like `big-scape`.
+The most straightforward way of installing is using Hatch.
+However, this does not allow you to run the application from anywhere using a command like `big-scape`.
 If you want to do that, follow the **Using Conda/Mamba** steps.
 
-### Using Docker
-
-TODO
-
 ### Using Hatch
 
-Install Hatch and setup an environment:
-
-1. `pip install hatch`
-2. `hatch -v env create bigscape`
+1. `git clone https://github.com/medema-group/BiG-SCAPE`.
+2. `cd BiG-SCAPE`
+3. `pip install hatch`
+4. `hatch -v env create bigscape`
 
 Run the application through hatch in the BiG-SCAPE folder:
 
@@ -50,18 +52,111 @@ This command only works inside the BiG-SCAPE folder.
 
 These steps use `mamba`.
 
-1. `mamba env create -f environment.yml`
-2. `mamba activate bigscape`
-3. `pip install .`
+Clone this repository:
+
+1. `git clone https://github.com/medema-group/BiG-SCAPE`.
+2. `cd BiG-SCAPE
+3. `mamba env create -f environment.yml`
+4. `mamba activate bigscape`
+5. `pip install .`
 
 You can now run bigscape anywhere:
 
 `bigscape --help`
 
+### Using Docker
+Run BiG-SCAPE through docker using the docker run command:
+
+```sh
+docker run \
+    --volume your_root_data_dir:/home/data \
+    --detatch=false \
+    --rm \
+    --user=$(id -u):$(id -g) \
+    TODO: DOCKER URL \
+    # arguments from here are the same as using bigscape.py normally
+    cluster \
+    -i /home/data/your_input \
+    -o /home/data/output_folder \
+    -p /home/data/pfam_folder/Pfam-A.hmm
+```
+
+`your_root_data_dir` must be a parent folder of your input, your Pfam and where you want
+to put your output.
+
+For example:
+
+```
+/home/example/data
+  ├ /input
+  |    ├ experiment_1/
+  |    |  └ sample_1/
+  |    |      ├ a.region001.gbk
+  |    |      └ a.region002.gbk
+  |    └ unrelated_folder_do_not_use/
+  ├ /output
+  └ /pfam
+      └ Pfam-A.hmm
+```
+
+Can use a command as such:
+
+```
+docker run \
+    --volume /home/example/data:/home/data \
+    --detatch=false \
+    --rm \
+    --user=$(id -u):$(id -g) \
+    TODO: DOCKER URL \
+    cluster \
+    -i /home/data/input/experiment_1 \
+    -o /home/data/output/experument_1 \
+    -p /home/data/pfam/Pfam-A.hmm
+```
+
 
 ## Dev instructions
 
-1. pip install -r dev-requirements.txt
-2. pre-commit install
-3. mkdocs build
-4. have fun!
+We appreciate any contributions!
+In order to setup a development environment, please follow the following steps:
+
+### Using mamba
+
+1. Install (micro)mamba
+2. `git clone https://github.com/medema-group/BiG-SCAPE`.
+3. `cd BiG-SCAPE`
+4. `mamba env create -f environment.yml`
+5. `mamba activate bigscape`
+6. `pip install . --extra dev`
+7. `pre-commit install`
+
+To run BiG-SCAPE:
+`python bigscape.py --help`
+
+You can use the `bigscape --help` runnable directly, but this must be re-installed each
+time you make a change to the codebase.
+
+To run tests:
+`python -m pytest`
+
+When developing, make sure to use the mamba environment you created (called bigscape).
+
+### Using hatch
+
+1. `pip install hatch`
+2. `git clone https://github.com/medema-group/BiG-SCAPE`.
+3. `cd BiG-SCAPE`
+4. `hatch env create dev`
+5. `hatch run dev:pre-commit install`
+
+To run BiG-SCAPE:
+
+`hatch run bigscape:dev --help`
+
+To run tests:
+
+`hatch test`
+
+These commands only work inside the BiG-SCAPE folder.
+
+When developing, make sure to use the hatch environment under .venv/dev.