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conda-environment.txt
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conda-environment.txt
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# 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 >= 3.5 changed the bundle format, which breaks hg push of TS repositories
mercurial<3.5
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
#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
#SVGFig
# Fabric and dependencies
Fabric
# We still pin these dependencies because of modifications to the upstream packages
# Can't use Whoosh latest due to a bug but need to backport a bugfix from a
# newer release.
#
# https://bitbucket.org/mchaput/whoosh/pull-requests/50/fix-lru-thread-safety/diff
#Whoosh==2.4.1+gx1
# Flexible BAM index naming
#pysam==0.8.4+gx1