From 3fdbaa3dec07078388ce63bdb1a6f9251ffeb3f1 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Thu, 18 Jan 2018 12:31:41 -0500
Subject: [PATCH] Regenerate galaxy.yml.sample and documentation for newly
 added/documented config options.

---
 config/galaxy.yml.sample            | 21 ++++++++
 doc/source/admin/galaxy_options.rst | 77 +++++++++++++++++++++++++++++
 2 files changed, 98 insertions(+)

diff --git a/config/galaxy.yml.sample b/config/galaxy.yml.sample
index 9911f4ab323..b49f9cff6b5 100644
--- a/config/galaxy.yml.sample
+++ b/config/galaxy.yml.sample
@@ -650,6 +650,21 @@ galaxy:
   # The URL linked by the "Support" link in the "Help" menu.
   #support_url: 'https://galaxyproject.org/support'
 
+  # Enable integration with a custom Biostar instance.
+  #biostar_url: null
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_key_name: null
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_key: null
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_enable_bug_reports: true
+
+  # Enable integration with a custom Biostar instance.
+  #biostar_never_authenticate: false
+
   # The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
   #citation_url: 'https://galaxyproject.org/citing-galaxy'
 
@@ -1044,6 +1059,12 @@ galaxy:
   # them).
   #user_library_import_symlink_whitelist: null
 
+  # In conjunction or alternatively, Galaxy can restrict user library
+  # imports to those files that the user can read (by checking basic
+  # unix permissions). For this to work, the username has to match the
+  # username on the filesystem.
+  #user_library_import_check_permissions: false
+
   # Allow admins to paste filesystem paths during upload. For libraries
   # this adds an option to the admin library upload tool allowing admins
   # to paste filesystem paths to files and directories in a box, and
diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index a5b8a34899c..d508627f824 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -1255,6 +1255,56 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~
+``biostar_url``
+~~~~~~~~~~~~~~~
+
+:Description:
+    Enable integration with a custom Biostar instance.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~
+``biostar_key_name``
+~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Enable integration with a custom Biostar instance.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~
+``biostar_key``
+~~~~~~~~~~~~~~~
+
+:Description:
+    Enable integration with a custom Biostar instance.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``biostar_enable_bug_reports``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Enable integration with a custom Biostar instance.
+:Default: ``true``
+:Type: bool
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``biostar_never_authenticate``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Enable integration with a custom Biostar instance.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~
 ``citation_url``
 ~~~~~~~~~~~~~~~~
@@ -1734,6 +1784,20 @@
 :Type: str
 
 
+~~~~~~~~~~~
+``logging``
+~~~~~~~~~~~
+
+:Description:
+    Controls where and how the server logs messages. If unset, the
+    default is to log all messages to standard output at the level
+    defined by the `log_level` configuration option. Configuration is
+    described in the documentation at:
+    https://docs.galaxyproject.org/en/master/admin/config_logging.html
+:Default: ``galaxy.config.LOGGING_CONFIG_DEFAULT``
+:Type: map
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``database_engine_option_echo``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -2140,6 +2204,19 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``user_library_import_check_permissions``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    In conjunction or alternatively, Galaxy can restrict user library
+    imports to those files that the user can read (by checking basic
+    unix permissions). For this to work, the username has to match the
+    username on the filesystem.
+:Default: ``false``
+:Type: bool
+
+
 ~~~~~~~~~~~~~~~~~~~~
 ``allow_path_paste``
 ~~~~~~~~~~~~~~~~~~~~