Commit 37d1acf3 authored by Lukas Jelonek's avatar Lukas Jelonek
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Update readme

parent 278b28bc
# 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
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
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