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Small galaxy related tweaks - another fix for flavor refactoring, set…

…ting defaults for more properties already being used, created a small helper method for configuring a standalone nginx server (i.e. independent of CloudMan).
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jmchilton committed Oct 11, 2012
1 parent 1919417 commit 5b010880b1f899fb5dd8be446d29ae90272cf110
Showing with 11 additions and 1 deletion.
  1. +10 −0 cloudbio/galaxy/__init__.py
  2. +1 −1 cloudbio/galaxy/tools.py
@@ -53,6 +53,11 @@ def _setup_galaxy_env_defaults(env):
env.galaxy_update_default = True
if "python_version" not in env:
env.python_version = "2.7" # Override in fabricrc if this is not the case.
+ if "galaxy_indices_mount" not in env:
+ indicies_dir = env.get("data_files", "/mnt/galaxyIndcies")
+ env.galaxy_indices_mount = indicies_dir
+ if "galaxy_data_mount" not in env:
+ env.galaxy_data_mount = "/mnt/galaxyData"
def _install_galaxy(env):
@@ -216,6 +221,11 @@ def _setup_nginx_service(env):
_setup_simple_service("nginx")
+def _install_nginx_standalone(env):
+ _install_nginx(env)
+ _setup_nginx_service(env)
+
+
def _install_nginx(env):
"""Nginx open source web server.
http://www.nginx.org/
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@@ -33,7 +33,7 @@ def _install_tools(env, tools_conf=None):
def _load_tools_conf(env):
tools_conf_path = env.get("galaxy_tools_conf",
os.path.join(env.config_dir, os.pardir,
- "contrib", "cloudman", "tools.yaml"))
+ "contrib", "flavor", "cloudman", "tools.yaml"))
with open(tools_conf_path) as in_handle:
full_data = yaml.load(in_handle)
return full_data

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