From 24872562ead2e63c6b51a21b11120b785e52f71b Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Sat, 8 Oct 2016 09:49:25 -0400
Subject: [PATCH] Fix bioconda support by adding conda-forge to default conda
channels.
xref https://github.com/galaxyproject/galaxy/pull/3023
---
galaxy/tools/deps/__init__.py | 4 ++--
galaxy/tools/deps/resolvers/conda.py | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/galaxy/tools/deps/__init__.py b/galaxy/tools/deps/__init__.py
index 7ba346c..8bac880 100644
--- a/galaxy/tools/deps/__init__.py
+++ b/galaxy/tools/deps/__init__.py
@@ -8,7 +8,7 @@
from galaxy.util import plugin_config
from .resolvers import NullDependency
-from .resolvers.conda import CondaDependencyResolver
+from .resolvers.conda import CondaDependencyResolver, DEFAULT_ENSURE_CHANNELS
from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver
from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver
@@ -21,7 +21,7 @@
'conda_prefix': None,
'conda_exec': None,
'conda_debug': None,
- 'conda_ensure_channels': 'r,bioconda,iuc',
+ 'conda_ensure_channels': DEFAULT_ENSURE_CHANNELS,
'conda_auto_install': False,
'conda_auto_init': False,
}
diff --git a/galaxy/tools/deps/resolvers/conda.py b/galaxy/tools/deps/resolvers/conda.py
index 9681a74..f16734a 100644
--- a/galaxy/tools/deps/resolvers/conda.py
+++ b/galaxy/tools/deps/resolvers/conda.py
@@ -30,7 +30,7 @@
DEFAULT_BASE_PATH_DIRECTORY = "_conda"
DEFAULT_CONDARC_OVERRIDE = "_condarc"
-DEFAULT_ENSURE_CHANNELS = "r,bioconda,iuc"
+DEFAULT_ENSURE_CHANNELS = "conda-forge,r,bioconda,iuc"
log = logging.getLogger(__name__)