From c8b0057349be9a683e295c073f66163f47c257e7 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 21 Jan 2016 16:03:51 -0500
Subject: [PATCH 1/2] Add a requirements file suitable for use with `conda
 {create,install} --file`.

---
 .../dependencies/conda-requirements.txt       | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 lib/galaxy/dependencies/conda-requirements.txt

diff --git a/lib/galaxy/dependencies/conda-requirements.txt b/lib/galaxy/dependencies/conda-requirements.txt
new file mode 100644
index 00000000000..9bec25a4058
--- /dev/null
+++ b/lib/galaxy/dependencies/conda-requirements.txt
@@ -0,0 +1,63 @@
+# 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==0.8.3+gx1

From 1486af0ef90a186b5648f737af32e84640263857 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Tue, 26 Jan 2016 16:46:20 -0500
Subject: [PATCH 2/2] Rename conda-requirements.txt to conda-environment.txt
 since it is not a requirements file, include instructions on how to install
 remaining dependencies from pip.

---
 ...-requirements.txt => conda-environment.txt} | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 rename lib/galaxy/dependencies/{conda-requirements.txt => conda-environment.txt} (56%)

diff --git a/lib/galaxy/dependencies/conda-requirements.txt b/lib/galaxy/dependencies/conda-environment.txt
similarity index 56%
rename from lib/galaxy/dependencies/conda-requirements.txt
rename to lib/galaxy/dependencies/conda-environment.txt
index 9bec25a4058..12d8e4853db 100644
--- a/lib/galaxy/dependencies/conda-requirements.txt
+++ b/lib/galaxy/dependencies/conda-environment.txt
@@ -1,3 +1,21 @@
+# 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