.gitignore

# Emacs rope configuration
.ropeproject
.project
.pydevproject
.settings
.ruffus_history.sqlite

# pyenv version file
.python-version

# Python
*.py[co]

# Compiled files
*.o

## Packages
*.egg
*.swp
*.egg-info
*.copy
dist
build
eggs
parts
copy.autoenv
internal
var
sdist
deb_dist
develop-eggs
.installed.cfg

## Installer logs
pip-log.txt

## Unit test / coverage reports
.coverage
.tox

## Translations
#*.mo

## paver generated files
# test analyis
pathDescTest

# Project ignores
snake-eater.ps
snake-eater.pdf
.config
.editorconfig
.ppt-version
docs/source/pathdiscov.rst
docs/source/pathdiscov.stages.rst
docs/source/pathdiscov.test.rst
pathdiscov/download/ray
pathdiscov/download/EMBOSS-6.6.0
pathdiscov/download/RayPlatform
pathdiscov/download/bwa
pathdiscov/download/samtools
pathdiscov/download/htslib
pathdiscov/bin
pathdiscov/lib
pathdiscov/include
pathdiscov/download/snap
lib64
man
virtualenv-1.11.6
pathdiscov/files/config.yaml
pathdiscov/files/config.yaml.bak
pathdiscov/config.yaml
pathdiscov/config.yaml.bak
pathdiscov/config.yaml.base
pathdiscov/files/settings.sh
pathdiscov/files/sample.param.bak
pathdiscov/files/settings.sh.bak
pathdiscov/files/sample.param
.vagrant
#pathdiscov/download/prinseq-lite-*
pathdiscov/download/bwa-*
pathdiscov/download/htslib-*
pathdiscov/download/samtools-*
pathdiscov/download/fastqc*
pathdiscov/download/.pip_cache
tests/test_runs
docs/pathdiscov

#Negate, include the file