# This file can be used with conda's `--file` option to install as many of
# Galaxy's dependencies as possible using Conda. The file
# conda-requirements.txt in this directory can be used to install the remaining
# missing dependencies using pip:
#
# $ conda create --name galaxy --file lib/galaxy/dependencies/conda-environment.txt
# $ source activate galaxy
# $ pip install --index-url=https://wheels.galaxyproject.org/simple/ -r lib/galaxy/dependencies/requirements.txt
#
# or if you already have an environment:
#
# $ source activate galaxy
# $ conda install --file lib/galaxy/dependencies/conda-environment.txt
# $ pip install --index-url=https://wheels.galaxyproject.org/simple/ -r lib/galaxy/dependencies/requirements.txt
#
# More details are available in the administration section of the Galaxy
# documentation at https://galaxy.readthedocs.org/

# packages with C extensions
# numpy should be installed before bx to enable extra features in bx
numpy
bx-python
MarkupSafe
PyYAML
SQLAlchemy
mercurial
pycrypto

# Install python_lzo if you want to support indexed access to lzo-compressed
# locally cached maf files via bx-python
#python_lzo

# pure Python packages
Paste
PasteDeploy
docutils
#wchartype
repoze.lru
Routes
WebOb
#WebHelpers
Mako
pytz
Babel
Whoosh
#Beaker

# Cheetah and dependencies
Cheetah

# BioBlend and dependencies
bioblend
boto
requests

# kombu and dependencies
#kombu

# sqlalchemy-migrate and dependencies
#sqlalchemy-migrate
decorator
#Tempita
sqlparse
six
#Parsley
nose
svgwrite

# Fabric and dependencies
Fabric

# We still pin these dependencies because of modifications to the upstream packages

# Flexible BAM index naming
#pysam==0.8.4+gx1
