diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
index c12c5799f01..7642b029429 100644
--- a/lib/galaxy/dependencies/pinned-requirements.txt
+++ b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -25,6 +25,9 @@ pytz==2015.4
 Babel==2.0
 Beaker==1.7.0
 dictobj==0.3.1
+nose==1.3.7
+Parsley==1.3
+six==1.9.0
 
 # Cheetah and dependencies
 Cheetah==2.4.4
@@ -51,16 +54,15 @@ decorator==4.0.2
 Tempita==0.5.3dev
 sqlparse==0.1.16
 pbr==1.8.0
-six==1.9.0
-Parsley==1.3
-nose==1.3.7
+
+# svgwrite and dependencies
 svgwrite==1.1.6
+pyparsing==2.1.1
 
 # 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.
diff --git a/lib/galaxy/dependencies/requirements.txt b/lib/galaxy/dependencies/requirements.txt
index 675cbc0964e..6c9f8119f7b 100644
--- a/lib/galaxy/dependencies/requirements.txt
+++ b/lib/galaxy/dependencies/requirements.txt
@@ -5,8 +5,7 @@ bx-python
 MarkupSafe
 PyYAML
 SQLAlchemy
-# Mercurial >= 3.5 changed the bundle format, which breaks hg push of TS repositories
-mercurial<3.5
+mercurial
 pycrypto
 
 # Install python_lzo if you want to support indexed access to lzo-compressed
@@ -27,14 +26,19 @@ pytz
 Babel
 Beaker
 dictobj
+nose
+Parsley
+six
 
 # Cheetah and dependencies
 Cheetah
+Markdown
 
 # BioBlend and dependencies
 bioblend
 boto
 requests
+requests-toolbelt
 
 # kombu and dependencies
 kombu
@@ -48,14 +52,16 @@ sqlalchemy-migrate
 decorator
 Tempita
 sqlparse
-six
-Parsley
-nose
+pbr
 
+# svgwrite and dependencies
 svgwrite
+pyparsing
 
 # Fabric and dependencies
 Fabric
+paramiko
+ecdsa
 
 # We still pin these dependencies because of modifications to the upstream packages