Merge branch 'release_18.09' into dev

client/package.json

@@ -73,7 +73,7 @@
     "babel-plugin-transform-vue-template": "^0.4.2",
     "babel-preset-env": "^1.7.0",
     "chai": "^4.1.2",
-    "concurrently": "^3.6.0",
+    "concurrently": "^4.0.1",
     "css-loader": "^0.28.11",
     "del": "^3.0.0",
     "expose-loader": "^0.7.5",

config/galaxy.yml.sample

@@ -100,7 +100,7 @@ galaxy:
   # path as the prefix in the filter above.  This value becomes the
   # "path" attribute set in the cookie so the cookies from each instance
   # will not clobber each other.
-  #cookie_path: null
+  #cookie_path: ''
 
   # By default, Galaxy uses a SQLite database at
   # 'database/universe.sqlite'.  You may use a SQLAlchemy connection
@@ -140,7 +140,7 @@ galaxy:
   # an existing template database. This will set that. This is probably
   # only useful for testing but documentation is included here for
   # completeness.
-  #database_template: null
+  #database_template: ''
 
   # Slow query logging.  Queries slower than the threshold indicated
   # below will be logged to debug.  A value of '0' is disabled.  For
@@ -240,7 +240,7 @@ galaxy:
 
   # conda channels to enable by default (https://conda.io/docs/user-
   # guide/tasks/manage-channels.html)
-  #conda_ensure_channels: 'iuc,bioconda,conda-forge,defaults'
+  #conda_ensure_channels: 'iuc,conda-forge,bioconda,defaults'
 
   # Set to True to instruct Galaxy to look for and install missing tool
   # dependencies before each job runs.
@@ -292,7 +292,7 @@ galaxy:
   # won't fail to load Galaxy if it is not and 'polling' which will use
   # a less efficient monitoring scheme that may work in wider range of
   # scenarios than the watchdog default.
-  #watch_tools: false
+  #watch_tools: 'false'
 
   # Set to True to enable monitoring of dynamic job rules. If changes
   # are found, rules are automatically reloaded. Takes the same values
@@ -325,7 +325,7 @@ galaxy:
   # container resolvers to use when discovering containers for Galaxy.
   # If this is set to None, the default containers loaded is determined
   # by enable_beta_mulled_containers.
-  #containers_resolvers_config_file: null
+  #containers_resolvers_config_file: ''
 
   # involucro is a tool used to build Docker containers for tools from
   # Conda dependencies referenced in tools as `requirement`s. The
@@ -391,7 +391,7 @@ galaxy:
   # won't fail to load Galaxy if it is not and 'polling' which will use
   # a less efficient monitoring scheme that may work in wider range of
   # scenarios than the watchdog default.
-  #watch_tool_data_dir: false
+  #watch_tool_data_dir: 'false'
 
   # File containing old-style genome builds
   #builds_file_path: tool-data/shared/ucsc/builds.txt
@@ -533,17 +533,17 @@ galaxy:
   # mail through an SMTP server, which you may define here (host:port).
   # Galaxy will automatically try STARTTLS but will continue upon
   # failure.
-  #smtp_server: null
+  #smtp_server: ''
 
   # If your SMTP server requires a username and password, you can
   # provide them here (password in cleartext here, but if your server
   # supports STARTTLS it will be sent over the network encrypted).
-  #smtp_username: null
+  #smtp_username: ''
 
   # If your SMTP server requires a username and password, you can
   # provide them here (password in cleartext here, but if your server
   # supports STARTTLS it will be sent over the network encrypted).
-  #smtp_password: null
+  #smtp_password: ''
 
   # If your SMTP server requires SSL from the beginning of the
   # connection
@@ -560,14 +560,14 @@ galaxy:
   # disabled if no address is set.  Also this email is shown as a
   # contact to user in case of Galaxy misconfiguration and other events
   # user may encounter.
-  #error_email_to: null
+  #error_email_to: ''
 
   # Email address to use in the 'From' field when sending emails for
   # account activations, workflow step notifications and password
   # resets. We recommend using string in the following format: Galaxy
   # Project <[email protected]> If not configured, '<galaxy-
   # no-reply@HOSTNAME>' will be used.
-  #email_from: null
+  #email_from: ''
 
   # URL of the support resource for the galaxy instance.  Used in
   # activation emails.
@@ -614,7 +614,7 @@ galaxy:
 
   # You can enter tracking code here to track visitor's behavior through
   # your Google Analytics account.  Example: UA-XXXXXXXX-Y
-  #ga_code: null
+  #ga_code: ''
 
   # Galaxy can display data at various external browsers.  These options
   # specify which browsers should be available.  URLs and builds
@@ -647,13 +647,13 @@ galaxy:
   #message_box_visible: false
 
   # Show a message box under the masthead.
-  #message_box_content: null
+  #message_box_content: ''
 
   # Show a message box under the masthead.
   #message_box_class: info
 
   # Append "/{brand}" to the "Galaxy" text in the masthead.
-  #brand: null
+  #brand: ''
 
   # Format string used when showing date and time information. The
   # string may contain: - the directives used by Python time.strftime()
@@ -704,13 +704,13 @@ galaxy:
   #support_url: 'https://galaxyproject.org/support/'
 
   # Enable integration with a custom Biostar instance.
-  #biostar_url: null
+  #biostar_url: ''
 
   # Enable integration with a custom Biostar instance.
-  #biostar_key_name: null
+  #biostar_key_name: ''
 
   # Enable integration with a custom Biostar instance.
-  #biostar_key: null
+  #biostar_key: ''
 
   # Enable integration with a custom Biostar instance.
   #biostar_enable_bug_reports: true
@@ -737,7 +737,7 @@ galaxy:
   # The URL linked by the "Terms and Conditions" link in the "Help"
   # menu, as well as on the user registration and login forms and in the
   # activation emails.
-  #terms_url: null
+  #terms_url: ''
 
   # The URL linked by the "Galaxy Q&A" link in the "Help" menu The
   # Galaxy Q&A site is under development; when the site is done, this
@@ -806,7 +806,7 @@ galaxy:
   # Redirect.  This should be set to the path defined in the nginx
   # config as an internal redirect with access to Galaxy's data files
   # (see documentation linked above).
-  #nginx_x_accel_redirect_base: null
+  #nginx_x_accel_redirect_base: ''
 
   # If using compression in the upstream proxy server, use this option
   # to disable gzipping of library .tar.gz and .zip archives, since the
@@ -828,24 +828,24 @@ galaxy:
   # in detail in the documentation linked above.  The upload store is a
   # temporary directory in which files uploaded by the upload module
   # will be placed.
-  #nginx_upload_store: null
+  #nginx_upload_store: ''
 
   # This value overrides the action set on the file upload form, e.g.
   # the web path where the nginx_upload_module has been configured to
   # intercept upload requests.
-  #nginx_upload_path: null
+  #nginx_upload_path: ''
 
   # Galaxy can also use nginx_upload_module to receive files staged out
   # upon job completion by remote job runners (i.e. Pulsar) that
   # initiate staging operations on the remote end.  See the Galaxy nginx
   # documentation for the corresponding nginx configuration.
-  #nginx_upload_job_files_store: null
+  #nginx_upload_job_files_store: ''
 
   # Galaxy can also use nginx_upload_module to receive files staged out
   # upon job completion by remote job runners (i.e. Pulsar) that
   # initiate staging operations on the remote end.  See the Galaxy nginx
   # documentation for the corresponding nginx configuration.
-  #nginx_upload_job_files_path: null
+  #nginx_upload_job_files_path: ''
 
   # Galaxy can upload user files in chunks without using nginx. Enable
   # the chunk uploader by specifying a chunk size larger than 0. The
@@ -910,7 +910,7 @@ galaxy:
   # Galaxy instead of a JSON or SQLite file for IPC. If you do not
   # specify this, it will be set randomly for you. You should set this
   # if you are managing the proxy manually.
-  #dynamic_proxy_golang_api_key: null
+  #dynamic_proxy_golang_api_key: ''
 
   # If True, Galaxy will attempt to configure a simple root logger if a
   # "loggers" section does not appear in this configuration file.
@@ -926,7 +926,7 @@ galaxy:
   # defined by the `log_level` configuration option. Configuration is
   # described in the documentation at:
   # https://docs.galaxyproject.org/en/master/admin/config_logging.html
-  #logging: galaxy.config.LOGGING_CONFIG_DEFAULT
+  #logging: null
 
   # Print database operations to the server log (warning, quite
   # verbose!).
@@ -985,7 +985,7 @@ galaxy:
   # and ending with /. E.g.
   # mysite.com,google.com,usegalaxy.org,/^[\w\.]*example\.com/ See:
   # https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
-  #allowed_origin_hostnames: null
+  #allowed_origin_hostnames: ''
 
   # Set the following to True to use Jupyter nbconvert to build HTML
   # from Jupyter notebooks in Galaxy histories.  This process may allow
@@ -1040,7 +1040,7 @@ galaxy:
   # errors will be sent to the indicated sentry instance.  This
   # connection string is available in your sentry instance under
   # <project_name> -> Settings -> API Keys.
-  #sentry_dsn: null
+  #sentry_dsn: ''
 
   # Sentry slow request logging.  Requests slower than the threshold
   # indicated below will be sent as events to the configured Sentry
@@ -1081,15 +1081,15 @@ galaxy:
 
   # Add an option to the library upload form which allows administrators
   # to upload a directory of files.
-  #library_import_dir: null
+  #library_import_dir: ''
 
   # Add an option to the library upload form which allows authorized
   # non-administrators to upload a directory of files.  The configured
   # directory must contain sub-directories named the same as the non-
   # admin user's Galaxy login ( email ).  The non-admin user is
   # restricted to uploading files or sub-directories of files contained
   # in their directory.
-  #user_library_import_dir: null
+  #user_library_import_dir: ''
 
   # If user_library_import_dir is set, this option will auto create a
   # library import directory for every user (based on their email) upon
@@ -1103,7 +1103,7 @@ galaxy:
   # user with library import permissions can import from anywhere in
   # these directories (assuming they are able to create symlinks to
   # them).
-  #user_library_import_symlink_whitelist: null
+  #user_library_import_symlink_whitelist: ''
 
   # In conjunction or alternatively, Galaxy can restrict user library
   # imports to those files that the user can read (by checking basic
@@ -1140,31 +1140,31 @@ galaxy:
   # higher the boost, the more importance the scoring algorithm gives to
   # the given field.  Section refers to the tool group in the tool
   # panel.  Rest of the fields are tool's attributes.
-  #tool_name_boost: 9
+  #tool_name_boost: 9.0
 
   # Boosts are used to customize this instance's toolbox search. The
   # higher the boost, the more importance the scoring algorithm gives to
   # the given field.  Section refers to the tool group in the tool
   # panel.  Rest of the fields are tool's attributes.
-  #tool_section_boost: 3
+  #tool_section_boost: 3.0
 
   # Boosts are used to customize this instance's toolbox search. The
   # higher the boost, the more importance the scoring algorithm gives to
   # the given field.  Section refers to the tool group in the tool
   # panel.  Rest of the fields are tool's attributes.
-  #tool_description_boost: 2
+  #tool_description_boost: 2.0
 
   # Boosts are used to customize this instance's toolbox search. The
   # higher the boost, the more importance the scoring algorithm gives to
   # the given field.  Section refers to the tool group in the tool
   # panel.  Rest of the fields are tool's attributes.
-  #tool_label_boost: 1
+  #tool_label_boost: 1.0
 
   # Boosts are used to customize this instance's toolbox search. The
   # higher the boost, the more importance the scoring algorithm gives to
   # the given field.  Section refers to the tool group in the tool
   # panel.  Rest of the fields are tool's attributes.
-  #tool_stub_boost: 5
+  #tool_stub_boost: 5.0
 
   # Boosts are used to customize this instance's toolbox search. The
   # higher the boost, the more importance the scoring algorithm gives to
@@ -1216,7 +1216,7 @@ galaxy:
   # method just returns bare usernames, set a default mail domain to be
   # appended to usernames, to become your Galaxy usernames (email
   # addresses).
-  #remote_user_maildomain: null
+  #remote_user_maildomain: ''
 
   # If use_remote_user is enabled, the header that the upstream proxy
   # provides the remote username in defaults to HTTP_REMOTE_USER (the
@@ -1236,7 +1236,7 @@ galaxy:
 
   # If use_remote_user is enabled, you can set this to a URL that will
   # log your users out.
-  #remote_user_logout_href: null
+  #remote_user_logout_href: ''
 
   # If your proxy and/or authentication source does not normalize e-mail
   # addresses or user names being passed to Galaxy - set the following
@@ -1255,7 +1255,7 @@ galaxy:
   # Admin section of the server, and will have access to create users,
   # groups, roles, libraries, and more.  For more information, see:
   # https://galaxyproject.org/admin/
-  #admin_users: null
+  #admin_users: ''
 
   # Force everyone to log in (disable anonymous access).
   #require_login: false
@@ -1438,7 +1438,7 @@ galaxy:
 
   # Optional list of email addresses of API users who can make calls on
   # behalf of other users.
-  #api_allow_run_as: null
+  #api_allow_run_as: ''
 
   # Master key that allows many API admin actions to be used without
   # actually having a defined admin user in the database/config.  Only
@@ -1470,11 +1470,11 @@ galaxy:
   # options. This should point to a directory containing subdirectories
   # matching users' identifier (defaults to e-mail), where Galaxy will
   # look for files.
-  #ftp_upload_dir: null
+  #ftp_upload_dir: ''
 
   # This should be the hostname of your FTP server, which will be
   # provided to users in the help text.
-  #ftp_upload_site: null
+  #ftp_upload_site: ''
 
   # User attribute to use as subdirectory in calculating default
   # ftp_upload_dir pattern. By default this will be email so a user's
@@ -1665,7 +1665,7 @@ galaxy:
   # prior to running tools.  This can be especially useful for running
   # jobs as the actual user, to remove the need to configure each user's
   # environment individually.
-  #environment_setup_file: null
+  #environment_setup_file: ''
 
   # Optional file containing job resource data entry fields definition.
   # These fields will be presented to users in the tool forms and allow
@@ -1761,3 +1761,8 @@ galaxy:
   # that should be always available.
   #persistent_communication_rooms: null
 
+  # Allow disabling pbkdf2 hashing of passwords for legacy situations.
+  # This should normally be left enabled unless there is a specific
+  # reason to disable it.
+  #use_pbkdf2: true
+

doc/source/admin/conda_faq.rst

@@ -227,9 +227,9 @@ Admin panel (under Tool Management → Manage dependencies).
 The simple answer is: you don't need to do much to make Conda work for a tool.
 
 The ``<requirement>`` tag in the tool XML file is enough. The name and the
-version should correspond to a Conda package in the ``default``, ``r``,
-``bioconda`` or ``iuc`` Conda channel (you can extend this list if you
-like in your ``galaxy.yml`` ). If this is the case you are ready to go. Read
+version should correspond to a Conda package in one of the enabled channels
+(which are specified by the ``conda_ensure_channels`` directive in
+``galaxy.yml`` ). If this is the case you are ready to go. Read
 more about `Conda channels`_  and browse their packages on https://anaconda.org/ url followed by the channel name (e.g.
 `https://anaconda.org/bioconda <https://anaconda.org/bioconda>`__
 ).
@@ -258,7 +258,7 @@ With Conda package manager installed on your system, run:
 
 .. code-block:: bash
 
-   $ conda search <package_name> -c bioconda -c iuc
+   $ conda search <package_name> -c iuc -c conda-forge -c bioconda
 
 This will search in all channels that are activated by default in
 Galaxy. If you find your package, you are ready to go. If not please

doc/source/admin/dependency_resolvers.rst

@@ -218,7 +218,7 @@ debug
 ensure_channels
     conda channels to enable by default. See
     https://conda.io/docs/user-guide/tasks/manage-channels.html for more
-    information about channels. This defaults to ``iuc,bioconda,conda-forge,defaults``.
+    information about channels. This defaults to ``iuc,conda-forge,bioconda,defaults``.
     This order should be consistent with the `Bioconda prescribed order <https://github.com/bioconda/bioconda-recipes/blob/master/config.yml>`__
     if it includes ``bioconda``.
 

doc/source/admin/framework_dependencies.rst

@@ -204,8 +204,8 @@ not run the script, the dependencies will simply be installed via pip.
 
 .. code-block:: console
 
-    $ conda config --add channels conda-forge
     $ conda config --add channels bioconda
+    $ conda config --add channels conda-forge
     $ conda create --name galaxy --file <(lib/galaxy/dependencies/conda-file.sh)
     Filtering out requirements not available in conda... done
     Solving environment: done