Merge pull request #12 from natefoo/mvdbeek-fix_galaxy_yml_prefix_com…

…ments

Slight rewording of the cookie_path option description, and corrections to file_path and new_file_path descriptions

config/galaxy.yml.sample

@@ -98,11 +98,11 @@ uwsgi:
 
 galaxy:
 
-  # If Galaxy is served at a URL prefix and you are running more than
-  # one Galaxy instance behind one hostname, you will want to set this
-  # to the same path as the prefix in the mount uWSGI configuration
-  # above. This value becomes the "path" attribute set in the cookie so
-  # the cookies from each instance will not clobber each other.
+  # When running multiple Galaxy instances under separate URL prefixes
+  # on a single hostname, you will want to set this to the same path as
+  # the prefix set in the uWSGI "mount" configuration option above. This
+  # value becomes the "path" attribute set in the cookie so the cookies
+  # from one instance will not clobber those from another.
   #cookie_path: ''
 
   # By default, Galaxy uses a SQLite database at
@@ -170,10 +170,13 @@ galaxy:
   # not recommended for production use.
   #database_auto_migrate: false
 
-  # Dataset files are stored in this directory.
+  # Where dataset files are stored. It must accessible at the same path
+  # on any cluster nodes that will run Galaxy jobs, unless using Pulsar.
   #file_path: database/files
 
-  # Temporary files are stored in this directory.
+  # Where temporary files are stored. It must accessible at the same
+  # path on any cluster nodes that will run Galaxy jobs, unless using
+  # Pulsar.
   #new_file_path: database/tmp
 
   # Tool config files, defines what tools are available in Galaxy. Tools

config/reports.yml.sample

@@ -80,12 +80,11 @@ uwsgi:
 
 reports:
 
-  # If Galaxy Reports is served at a URL prefix and you are running more
-  # than one Galaxy Reports instance behind one hostname, you will want
-  # to set this to the same path as the prefix in the mount uWSGI
-  # configuration above. This value becomes the "path" attribute set in
-  # the cookie so the cookies from each instance will not clobber each
-  # other.
+  # When running multiple Galaxy Reports instances under separate URL
+  # prefixes on a single hostname, you will want to set this to the same
+  # path as the prefix set in the uWSGI "mount" configuration option
+  # above. This value becomes the "path" attribute set in the cookie so
+  # the cookies from one instance will not clobber those from another.
   #cookie_path: null
 
   # Verbosity of console log messages.  Acceptable values can be found
@@ -98,12 +97,10 @@ reports:
   # external database.
   #database_connection: 'sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE'
 
-  # Where dataset files are saved. Temporary storage for additional
-  # datasets, this should be shared through the cluster.
+  # Where dataset files are stored.
   #file_path: database/files
 
-  # Where dataset files are saved. Temporary storage for additional
-  # datasets, this should be shared through the cluster.
+  # Where temporary files are stored.
   #new_file_path: database/tmp
 
   # Mako templates are compiled as needed and cached for reuse, this

config/tool_shed.yml.sample

@@ -98,8 +98,7 @@ tool_shed:
   # Where Tool Shed repositories are stored.
   #file_path: database/community_files
 
-  # Temporary storage for additional datasets, this should be shared
-  # through the cluster
+  # Where temporary files are stored.
   #new_file_path: database/tmp
 
   # File containing old-style genome builds
@@ -351,12 +350,11 @@ tool_shed:
   # store this information.
   #citation_cache_lock_dir: database/citations/lock
 
-  # If the Tool Shed is served at a URL prefix and you are running more
-  # than one Tool Shed instance behind one hostname, you will want to
-  # set this to the same path as the prefix in the mount uWSGI
-  # configuration above. This value becomes the "path" attribute set in
-  # the cookie so the cookies from each instance will not clobber each
-  # other.
+  # When running multiple Tool Shed instances under separate URL
+  # prefixes on a single hostname, you will want to set this to the same
+  # path as the prefix set in the uWSGI "mount" configuration option
+  # above. This value becomes the "path" attribute set in the cookie so
+  # the cookies from one instance will not clobber those from another.
   #cookie_path: null
 
   # Enable authentication via OpenID.  Allows users to log in to their

doc/source/admin/galaxy_options.rst

@@ -3,11 +3,11 @@
 ~~~~~~~~~~~~~~~
 
 :Description:
-    If Galaxy is served at a URL prefix and you are running more than
-    one Galaxy instance behind one hostname, you will want to set this
-    to the same path as the prefix in the mount uWSGI configuration
-    above. This value becomes the "path" attribute set in the cookie
-    so the cookies from each instance will not clobber each other.
+    When running multiple Galaxy instances under separate URL prefixes
+    on a single hostname, you will want to set this to the same path
+    as the prefix set in the uWSGI "mount" configuration option above.
+    This value becomes the "path" attribute set in the cookie so the
+    cookies from one instance will not clobber those from another.
 :Default: ````
 :Type: str
 
@@ -161,7 +161,9 @@
 ~~~~~~~~~~~~~
 
 :Description:
-    Dataset files are stored in this directory.
+    Where dataset files are stored. It must accessible at the same
+    path on any cluster nodes that will run Galaxy jobs, unless using
+    Pulsar.
 :Default: ``database/files``
 :Type: str
 
@@ -171,7 +173,9 @@
 ~~~~~~~~~~~~~~~~~
 
 :Description:
-    Temporary files are stored in this directory.
+    Where temporary files are stored. It must accessible at the same
+    path on any cluster nodes that will run Galaxy jobs, unless using
+    Pulsar.
 :Default: ``database/tmp``
 :Type: str
 

doc/source/admin/reports_options.rst

@@ -3,12 +3,12 @@
 ~~~~~~~~~~~~~~~
 
 :Description:
-    If Galaxy Reports is served at a URL prefix and you are running
-    more than one Galaxy Reports instance behind one hostname, you
-    will want to set this to the same path as the prefix in the mount
-    uWSGI configuration above. This value becomes the "path" attribute
-    set in the cookie so the cookies from each instance will not
-    clobber each other.
+    When running multiple Galaxy Reports instances under separate URL
+    prefixes on a single hostname, you will want to set this to the
+    same path as the prefix set in the uWSGI "mount" configuration
+    option above. This value becomes the "path" attribute set in the
+    cookie so the cookies from one instance will not clobber those
+    from another.
 :Default: ``None``
 :Type: str
 
@@ -43,8 +43,7 @@
 ~~~~~~~~~~~~~
 
 :Description:
-    Where dataset files are saved. Temporary storage for additional
-    datasets, this should be shared through the cluster.
+    Where dataset files are stored.
 :Default: ``database/files``
 :Type: str
 
@@ -54,8 +53,7 @@
 ~~~~~~~~~~~~~~~~~
 
 :Description:
-    Where dataset files are saved. Temporary storage for additional
-    datasets, this should be shared through the cluster.
+    Where temporary files are stored.
 :Default: ``database/tmp``
 :Type: str
 

lib/galaxy/webapps/galaxy/config_schema.yml

@@ -30,10 +30,11 @@ mapping:
         default: ''
         required: false
         desc: |
-          If Galaxy is served at a URL prefix and you are running more than one Galaxy instance
-          behind one hostname, you will want to set this to the same path as the prefix
-          in the mount uWSGI configuration above. This value becomes the "path" attribute set in the
-          cookie so the cookies from each instance will not clobber each other.
+          When running multiple Galaxy instances under separate URL prefixes on a
+          single hostname, you will want to set this to the same path as the prefix set
+          in the uWSGI "mount" configuration option above. This value becomes the "path"
+          attribute set in the cookie so the cookies from one instance will not clobber
+          those from another.
 
       database_connection:
         type: str
@@ -143,14 +144,16 @@ mapping:
         default: database/files
         required: false
         desc: |
-          Dataset files are stored in this directory.
+          Where dataset files are stored. It must accessible at the same path on any cluster
+          nodes that will run Galaxy jobs, unless using Pulsar.
 
       new_file_path:
         type: str
         default: database/tmp
         required: false
         desc: |
-          Temporary files are stored in this directory.
+          Where temporary files are stored. It must accessible at the same path on any cluster
+          nodes that will run Galaxy jobs, unless using Pulsar.
 
       tool_config_file:
         type: str

lib/galaxy/webapps/reports/config_schema.yml

@@ -10,10 +10,11 @@ mapping:
       cookie_path:
         type: str
         desc: |
-          If Galaxy Reports is served at a URL prefix and you are running more than one Galaxy Reports instance
-          behind one hostname, you will want to set this to the same path as the prefix
-          in the mount uWSGI configuration above. This value becomes the "path" attribute set in the
-          cookie so the cookies from each instance will not clobber each other.
+          When running multiple Galaxy Reports instances under separate URL prefixes on a
+          single hostname, you will want to set this to the same path as the prefix set
+          in the uWSGI "mount" configuration option above. This value becomes the "path"
+          attribute set in the cookie so the cookies from one instance will not clobber
+          those from another.
       
       log_level:
         type: str
@@ -35,15 +36,13 @@ mapping:
         type: str
         default: database/files
         desc: |
-          Where dataset files are saved.
-          Temporary storage for additional datasets, this should be shared through the cluster.
+          Where dataset files are stored.
       
       new_file_path:
         type: str
         default: database/tmp
         desc: |
-          Where dataset files are saved.
-          Temporary storage for additional datasets, this should be shared through the cluster.
+          Where temporary files are stored.
       
       template_cache_path:
         type: str

lib/galaxy/webapps/tool_shed/config_schema.yml

@@ -44,8 +44,7 @@ mapping:
         default: database/tmp
         required: false
         desc: |
-          Temporary storage for additional datasets,
-          this should be shared through the cluster
+          Where temporary files are stored.
       
       builds_file_path:
         type: str
@@ -521,10 +520,11 @@ mapping:
         default: null
         required: false
         desc: |
-          If the Tool Shed is served at a URL prefix and you are running more than one Tool Shed instance
-          behind one hostname, you will want to set this to the same path as the prefix
-          in the mount uWSGI configuration above. This value becomes the "path" attribute set in the
-          cookie so the cookies from each instance will not clobber each other.
+          When running multiple Tool Shed instances under separate URL prefixes on a
+          single hostname, you will want to set this to the same path as the prefix set
+          in the uWSGI "mount" configuration option above. This value becomes the "path"
+          attribute set in the cookie so the cookies from one instance will not clobber
+          those from another.
 
       enable_openid:
         type: bool