Merge branch 'release/1.0.0'

First working release

Author: sb43

.dockerignore

@@ -0,0 +1,8 @@
+/LICENCE
+/INSTALL
+/CHANGES.md
+/.gitignore
+/.git
+/.travis.yml
+/env
+/dist

CHANGES.md

@@ -1,3 +1,3 @@
 ## 1.0.0
-* First commit
+* First working release
 

README.md

@@ -24,7 +24,8 @@ This project hosts scripts to annotate VCF files using user defined driver genes
 <!-- /TOC -->
 
 ## Design
-Uses [bcftools] and tabix from htslib
+
+Uses [bcftools], [tabix] and [bgzip] in user's path , these are part of [htslib] or can be installed separately
 
 ## Tools
 
@@ -59,10 +60,6 @@ pip install annotateVcf.X.X.X-py3-none-any.whl
 
 Release `.whl` files are generated as part of the release process and can be found on the [release page][annotateVcf-releases]
 
-### Package Dependancies
-
-`pip` will install the relevant dependancies, listed here for convenience, please refer requirements.txt for versions.
-
 ## Development environment
 
 This project uses git pre-commit hooks.  As these will execute on your system it
@@ -136,9 +133,11 @@ pip install --find-links=~/wheels annotateVcf
 
 ### Reference
 <!--refs-->
- [bcftools]: http://samtools.github.io/bcftools/bcftools.html 
+ [htslib]: https://github.com/samtools/htslib
+ [bcftools]: https://github.com/samtools/bcftools
+ [tabix]: https://github.com/samtools/tabix
  [VAGrENT]: https://github.com/cancerit/VAGrENT 
- [travis-master-badge]: https://travis-ci.org/cancerit/annotateVcf.svg?branch=master
- [travis-develop-badge]: https://travis-ci.org/cancerit/annotateVcf.svg?branch=develop
+ [travis-master-badge]: https://travis-ci.org/cancerit/annotateVCF.svg?branch=master
+ [travis-develop-badge]: https://travis-ci.org/cancerit/annotateVCF.svg?branch=develop
  [travis-repo]: https://travis-ci.org/cancerit/annotateVcf
- [annotateVcf-releases]: https://github.com/cancerit/annotateVcf/releases
+ [annotateVcf-releases]: https://github.com/cancerit/annotateVCF/releases

requirements.txt

@@ -12,7 +12,7 @@
     'python_requires': '>= 3.3',
     'install_requires': ['tzlocal'],
     'packages': ['annotate'],
-    'package_data': {'annotate':['config/*.conf','config/drvData/*']},
+    'package_data': {'annotate':['config/*.conf','config/*.json','config/drvData/*']},
     'entry_points': {
         'console_scripts': ['annotateVcf=annotate.annotate_cmd:main'],
     }