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requirements.txt
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requirements.txt
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# 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