Pin requirements

requirements.txt

@@ -1,5 +1,5 @@
 # packages with C extensions
-Cheetah=2.4.4
+Cheetah==2.4.4
 bx-python==0.7.3
 MarkupSafe==0.23
 PyYAML==3.11
@@ -7,38 +7,57 @@ SQLAlchemy==1.0.6
 mercurial==3.4.2
 numpy==1.9.2
 pycrypto==2.6.1
+python_lzo==1.8
+psycopg2==2.6.1
+
+# extra functionality from Dannon
+pysam==0.8.3gx1
+
+# Optional (prebuilt)
+
+# Optional (DIY)
+#MySQL_python
+#PyRods
+#pbs_python
 
 # pure Python packages
+bioblend==0.6.1
+Paste==1.7.5.1
+PasteDeploy==1.5.2
+docutils==0.12
+wchartype==0.1
+amqp==1.4.6
+repoze.lru==0.6
+Routes==2.2
+WebOb==1.4.1
+WebHelpers==1.3
+anyjson==0.3.3
+kombu==3.0.26
+Mako==1.0.2
+pytz==2015.4
+Babel==2.0
+Beaker==1.7.0
 
-# TODO
-Paste
-PasteDeploy
-docutils
-wchartype
-pexpect
-amqp
-repoze.lru
-Routes
-WebOb
-WebHelpers
-anyjson
-kombu
-pysam
-Mako
-pytz
-Babel
-decorator
-Tempita
-sqlalchemy-migrate
-Beaker
-Whoosh<2.5
-paramiko
-ssh
-Fabric
-boto
-simplejson
-bioblend
-Parsley
-WebError
-http://svgfig.googlecode.com/files/svgfig-1.1.6.tgz
-nose
+# sqlalchemy-migrate and dependencies
+sqlalchemy-migrate==0.10.0
+decorator==4.0.2
+Tempita==0.5.3dev
+sqlparse==0.1.16
+pbr==1.8.0
+six==1.9.0
+Parsley==1.3
+WebError==0.11
+nose==1.3.7
+SVGFig==1.1.6
+
+# Fabric and dependencies
+Fabric==1.10.2
+paramiko==1.15.2
+ecdsa==0.13
+# pycrypto, but it is a direct Galaxy dependency as well
+
+# 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==2.4.1gx1