Commit 2733b102 authored by Lukas Jelonek's avatar Lukas Jelonek
Browse files

Convert readme to rst. Add licence to setup.cfg

parent 6dd71f50
# DB XREF resolver and retriever tool
DB XREF resolver and retriever tool
===================================
A tool that resolves database cross references (dbxrefs). It can return a list of
locations where the cross reference points to in different formats, like HTML,
......@@ -9,40 +10,47 @@ The intended audience for this tool are bioinformatician that need to collect
data for dbxrefs and postprocess it. By returning everything in json format the
need for normalization and special parsing of the data is reduced.
# Getting started for development (Setup)
Getting started for development (Setup)
---------------------------------------
Prerequisites:
* git
* python3
Supported bioinformatic databases:
Supported databases:
* Ontologies
* Gene Ontology
* Enzyme
* Gene Identifier
* Uniprot
* Taxonomy
* SequenceOntology
* RFAM
* Pubmed
* Protein Families
* PDB
* InterPro
* GeneID
* Gene Ontology
* HTTP
Checkout the repository:
~~~~
git clone git@git.computational.bio.uni-giessen.de:SOaAS/dbxref.git
~~~~
Checkout the repository::
Setup a virtualenv for development and install it in editable mode:
git clone git@git.computational.bio.uni-giessen.de:SOaAS/dbxref.git
~~~~
# install in development environment
virtualenv --python=python3 venv; source venv/bin/activate;
pip install -e .
Setup a virtualenv for development and install it in editable mode::
# run tests
python3 setup.py test
# install in development environment
virtualenv --python=python3 venv; source venv/bin/activate;
pip install -e .
# compile documentation
python3 setup.py build_sphinx
~~~~
# run tests
python3 setup.py test
Use the application:
# compile documentation
python3 setup.py build_sphinx
~~~~
dbxref resolve GO:0097281
~~~~
Use the application::
dbxref resolve GO:0097281
......@@ -3,11 +3,11 @@ name = dbxref
author = Lukas Jelonek
author-email = Lukas.Jelonek@computational.bio.uni-giessen.de
description = A library for resolving database cross references
description-file = README.md
description-content-type = text/markdown; charset=UTF-8
description-file = README.rst
project_urls =
Source Code = https://git.computational.bio.uni-giessen.de/SOaAS/dbxref
keywords = dbxref
license = MIT
[files]
packages = dbxref
......
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