Update readme

README.md

-# Protein Sequence Observation Tool
-
-A tool that executes several bioinformatic tools for a set of protein
-sequences. The results of all tools are converted into json documents, enabling
-for simple post processing.
-
-# Getting started (Setup)
-
-Prerequisites:
-
-* git
-* python3
-* nextflow
-
-Supported bioinformatic tools:
-
-* hmmer
-* blastp
-* signalp
-* ghostx
-* targetp
-
-Install nextflow:
-
-~~~~
-curl -fsSL get.nextflow.io | bash 
-~~~~
-
-Checkout the repository:
-
-~~~~
-git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git
-~~~~
-
-# Configuration
-
-In the installation directory is a config.yaml file, that is used to override the paths to the 
-bioinformatic tools and that is used to specify the available profiles. 
-
-TODO write more about the structure of a profile
-
-
-# How to create a new module?
-
-TODO write what is a module
-TODO write about module configuration

README.rst

+Protein Sequence Observation Tool
+=================================
+
+A tool that executes several bioinformatic tools for a set of protein
+sequences. The results of all tools are converted into json documents, enabling
+for simple post processing.
+
+# Getting started for development (Setup)
+
+Prerequisites:
+
+* git
+* python3
+* nextflow
+
+Supported bioinformatic tools:
+
+* hmmer
+* blastp
+* signalp
+* ghostx
+* targetp
+
+Install nextflow::
+
+    curl -fsSL get.nextflow.io | bash 
+
+Checkout the repository::
+
+    git clone git@git.computational.bio.uni-giessen.de:SOaAS/psot.git
+
+Setup a virtualenv for development and install it in editable mode::
+
+    # install in development environment
+    virtualenv --python=python3 venv; source venv/bin/activate;
+    pip install -e .
+
+    # run tests
+    python3 setup.py test
+
+    # compile documentation
+    python3 setup.py build_sphinx
+
+At the moment the required `dbxref` module is not available via a public pip
+repository. You have to check it out via git and install it to the same virtual
+environment.
+
+Use the application::
+
+    psot analyze -f example/proteins.fas -o results -p fast
+
+
+Run the tests::
+    
+    # all tests
+    python3 setup.py test
+
+    # single tests module, e.g. test_repository
+    python3 setup.py test -s tests.test_repository