1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/1a56c4b28c6b/ changeset: 1a56c4b28c6b user: rmarenco date: 2012-09-07 15:54:31 summary: Modified the good files instead of the auto-generated ones affected #: 5 files

diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb database/compiled_templates/webapps/galaxy/base_panels.mako.py --- a/database/compiled_templates/webapps/galaxy/base_panels.mako.py +++ /dev/null @@ -1,415 +0,0 @@ -# -*- encoding:ascii -*- -from mako import runtime, filters, cache -UNDEFINED = runtime.UNDEFINED -__M_dict_builtin = dict -__M_locals_builtin = locals -_magic_number = 6 -_modified_time = 1346972736.51736 -_template_filename=u'templates/webapps/galaxy/base_panels.mako' -_template_uri=u'/webapps/galaxy/base_panels.mako' -_template_cache=cache.Cache(__name__, _modified_time) -_source_encoding='ascii' -_exports = ['masthead', 'javascripts', 'title'] - - -def _mako_get_namespace(context, name): - try: - return context.namespaces[(__name__, name)] - except KeyError: - _mako_generate_namespaces(context) - return context.namespaces[(__name__, name)] -def _mako_generate_namespaces(context): - pass -def _mako_inherit(template, context): - _mako_generate_namespaces(context) - return runtime._inherit_from(context, u'/base_panels.mako', _template_uri) -def render_body(context,**pageargs): - context.caller_stack._push_frame() - try: - __M_locals = __M_dict_builtin(pageargs=pageargs) - __M_writer = context.writer() - # SOURCE LINE 1 - __M_writer(u'\n\n') - # SOURCE LINE 4 - __M_writer(u'\n\n') - # SOURCE LINE 8 - __M_writer(u'\n\n') - # SOURCE LINE 232 - __M_writer(u'\n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_masthead(context): - context.caller_stack._push_frame() - try: - AssertionError = context.get('AssertionError', UNDEFINED) - h = context.get('h', UNDEFINED) - app = context.get('app', UNDEFINED) - util = context.get('util', UNDEFINED) - def tab(id,display,href,target='_parent',visible=True,extra_class='',menu_options=None): - context.caller_stack._push_frame() - try: - self = context.get('self', UNDEFINED) - len = context.get('len', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 19 - __M_writer(u'\n') - # SOURCE LINE 22 - __M_writer(u' \n ') - # SOURCE LINE 23 - - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "<b class='caret'></b>" - style = "" - if not visible: - style = "display: none;" - - - # SOURCE LINE 38 - __M_writer(u'\n <li class="') - # SOURCE LINE 39 - __M_writer(unicode(cls)) - __M_writer(u'" style="') - __M_writer(unicode(style)) - __M_writer(u'">\n') - # SOURCE LINE 40 - if href: - # SOURCE LINE 41 - __M_writer(u' <a class="') - __M_writer(unicode(a_cls)) - __M_writer(u'" data-toggle="dropdown" target="') - __M_writer(unicode(target)) - __M_writer(u'" href="') - __M_writer(unicode(href)) - __M_writer(u'">') - __M_writer(unicode(display)) - __M_writer(unicode(extra)) - __M_writer(u'</a>\n') - # SOURCE LINE 42 - else: - # SOURCE LINE 43 - __M_writer(u' <a class="') - __M_writer(unicode(a_cls)) - __M_writer(u'" data-toggle="dropdown">') - __M_writer(unicode(display)) - __M_writer(unicode(extra)) - __M_writer(u'</a>\n') - pass - # SOURCE LINE 45 - if menu_options: - # SOURCE LINE 46 - __M_writer(u' <ul class="dropdown-menu">\n') - # SOURCE LINE 47 - for menu_item in menu_options: - # SOURCE LINE 48 - if not menu_item: - # SOURCE LINE 49 - __M_writer(u' <li class="divider"></li>\n') - # SOURCE LINE 50 - else: - # SOURCE LINE 51 - __M_writer(u' <li>\n') - # SOURCE LINE 52 - if len ( menu_item ) == 1: - # SOURCE LINE 53 - __M_writer(u' ') - __M_writer(unicode(menu_item[0])) - __M_writer(u'\n') - # SOURCE LINE 54 - elif len ( menu_item ) == 2: - # SOURCE LINE 55 - __M_writer(u' ') - name, link = menu_item - - __M_writer(u'\n <a href="') - # SOURCE LINE 56 - __M_writer(unicode(link)) - __M_writer(u'">') - __M_writer(unicode(name)) - __M_writer(u'</a>\n') - # SOURCE LINE 57 - else: - # SOURCE LINE 58 - __M_writer(u' ') - name, link, target = menu_item - - __M_writer(u'\n <a target="') - # SOURCE LINE 59 - __M_writer(unicode(target)) - __M_writer(u'" href="') - __M_writer(unicode(link)) - __M_writer(u'">') - __M_writer(unicode(name)) - __M_writer(u'</a>\n') - pass - # SOURCE LINE 61 - __M_writer(u' </li>\n') - pass - pass - # SOURCE LINE 64 - __M_writer(u' </ul>\n') - pass - # SOURCE LINE 66 - __M_writer(u' </li>\n ') - return '' - finally: - context.caller_stack._pop_frame() - trans = context.get('trans', UNDEFINED) - _ = context.get('_', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 11 - __M_writer(u'\n\n') - # SOURCE LINE 14 - __M_writer(u' <div style="position: relative; right: -50%; float: left;">\n <div style="display: block; position: relative; right: 50%;">\n\n <ul class="nav" border="0" cellspacing="0">\n \n ') - # SOURCE LINE 67 - __M_writer(u'\n\n') - # SOURCE LINE 70 - __M_writer(u' ') - __M_writer(unicode(tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 73 - __M_writer(u' ') - __M_writer(unicode(tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 76 - __M_writer(u' ') - - menu_options = [ - [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], - None, - [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], - [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], - [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], - [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] - ] - tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) - - - # SOURCE LINE 86 - __M_writer(u'\n \n') - # SOURCE LINE 89 - __M_writer(u' ') - - menu_options = [ - [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], - [ _('Find Samples'), h.url_for( controller='/requests', action='find_samples_index' ) ], - [ _('Help'), app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] - ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) - - - # SOURCE LINE 96 - __M_writer(u'\n\n') - # SOURCE LINE 99 - __M_writer(u' ') - - menu_options = [ - [_('New Visualization'), h.url_for( controller='/tracks', action='index' ) ], - [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' ) ] - ] - tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list'), menu_options=menu_options ) - - - # SOURCE LINE 105 - __M_writer(u'\n\n') - # SOURCE LINE 108 - if app.config.get_bool( 'enable_cloud_launch', False ): - # SOURCE LINE 109 - __M_writer(u' ') - - menu_options = [ - [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], - ] - tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) - - - # SOURCE LINE 114 - __M_writer(u'\n') - pass - # SOURCE LINE 116 - __M_writer(u'\n') - # SOURCE LINE 118 - __M_writer(u' ') - __M_writer(unicode(tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) ))) - __M_writer(u'\n \n') - # SOURCE LINE 121 - __M_writer(u' ') - - menu_options = [ - [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8080/" ), "galaxy_main" ], - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] - ] - if app.config.get( 'terms_url', None ) is not None: - menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) - tab( "help", _("Help"), None, menu_options=menu_options) - - - # SOURCE LINE 132 - __M_writer(u'\n \n') - # SOURCE LINE 135 - __M_writer(u' ') - - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - if app.config.require_login: - logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) - else: - logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - - - # SOURCE LINE 172 - __M_writer(u'\n \n') - # SOURCE LINE 176 - __M_writer(u' </ul>\n\n </div>\n </div>\n \n') - # SOURCE LINE 182 - __M_writer(u' <div class="title">\n <a href="') - # SOURCE LINE 183 - __M_writer(unicode(h.url_for( app.config.get( 'logo_url', '/' ) ))) - __M_writer(u'">\n <img border="0" src="') - # SOURCE LINE 184 - __M_writer(unicode(h.url_for('/static/images/galaxyIcon_noText.png'))) - __M_writer(u'">\n Galaxy\n') - # SOURCE LINE 186 - if app.config.brand: - # SOURCE LINE 187 - __M_writer(u' <span>/ ') - __M_writer(unicode(app.config.brand)) - __M_writer(u'</span>\n') - pass - # SOURCE LINE 189 - __M_writer(u' </a>\n </div>\n\n') - # SOURCE LINE 193 - __M_writer(u' ') - - bar_style = "quota-meter-bar" - usage = 0 - percent = 0 - quota = None - try: - usage = trans.app.quota_agent.get_usage( trans=trans ) - quota = trans.app.quota_agent.get_quota( trans.user ) - percent = trans.app.quota_agent.get_percent( usage=usage, quota=quota ) - if percent is not None: - if percent >= 100: - bar_style += " quota-meter-bar-error" - elif percent >= 85: - bar_style += " quota-meter-bar-warn" - else: - percent = 0 - except AssertionError: - pass # Probably no history yet - tooltip = None - if not trans.user and quota and trans.app.config.allow_user_creation: - if trans.app.quota_agent.default_registered_quota is None or trans.app.quota_agent.default_unregistered_quota < trans.app.quota_agent.default_registered_quota: - tooltip = "Your disk quota is %s. You can increase your quota by registering a Galaxy account." % util.nice_size( quota ) - - - # SOURCE LINE 215 - __M_writer(u'\n\n <div class="quota-meter-container">\n') - # SOURCE LINE 218 - if tooltip: - # SOURCE LINE 219 - __M_writer(u' <div id="quota-meter" class="quota-meter tooltip" title="') - __M_writer(unicode(tooltip)) - __M_writer(u'">\n') - # SOURCE LINE 220 - else: - # SOURCE LINE 221 - __M_writer(u' <div id="quota-meter" class="quota-meter">\n') - pass - # SOURCE LINE 223 - __M_writer(u' <div id="quota-meter-bar" class="') - __M_writer(unicode(bar_style)) - __M_writer(u'" style="width: ') - __M_writer(unicode(percent)) - __M_writer(u'px;"></div>\n') - # SOURCE LINE 224 - if quota is not None: - # SOURCE LINE 225 - __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') - __M_writer(unicode(percent)) - __M_writer(u'%</div>\n') - # SOURCE LINE 226 - else: - # SOURCE LINE 227 - __M_writer(u' <div id="quota-meter-text" class="quota-meter-text">Using ') - __M_writer(unicode(util.nice_size( usage ))) - __M_writer(u'</div>\n') - pass - # SOURCE LINE 229 - __M_writer(u' </div>\n </div>\n \n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_javascripts(context): - context.caller_stack._push_frame() - try: - parent = context.get('parent', UNDEFINED) - __M_writer = context.writer() - # SOURCE LINE 6 - __M_writer(u'\n ') - # SOURCE LINE 7 - __M_writer(unicode(parent.javascripts())) - __M_writer(u'\n') - return '' - finally: - context.caller_stack._pop_frame() - - -def render_title(context): - context.caller_stack._push_frame() - try: - __M_writer = context.writer() - # SOURCE LINE 4 - __M_writer(u'Galaxy') - return '' - finally: - context.caller_stack._pop_frame() - -

diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ b/templates/webapps/community/base_panels.mako @@ -71,7 +71,8 @@

## Help tab. <% - menu_options = [ + menu_options = [ + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8081/" ), "_blank" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],

diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -120,7 +120,7 @@ ## Help tab. <% menu_options = [ - [_('Galaxy Q&A'), app.config.get( "q&a", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], + [_('Galaxy Q&A'), app.config.get( "qa_url", "http://slyfox.bx.psu.edu:8081/" ), "galaxy_main" ], [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], [_('Galaxy Wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],

diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb universe_wsgi.ini --- a/universe_wsgi.ini +++ /dev/null @@ -1,753 +0,0 @@ -# -# Galaxy is configured by default to be useable in a single-user development -# environment. To tune the application for a multi-user production -# environment, see the documentation at: -# -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server -# - -# Throughout this sample configuration file, except where stated otherwise, -# uncommented values override the default if left unset, whereas commented -# values are set to the default value. -# Examples of many of these options are explained in more detail in the wiki: -# -# http://wiki.g2.bx.psu.edu/Admin/Config -# -# Config hackers are encouraged to check there before asking for help. - -# ---- HTTP Server ---------------------------------------------------------- - -# Configuration of the internal HTTP server. - -[server:main] - -# The internal HTTP server to use. Currently only Paste is provided. This -# option is required. -use = egg:Paste#http - -# The port on which to listen. -#port = 8080 - -# The address on which to listen. By default, only listen to localhost (Galaxy -# will not be accessible over the network). Use '0.0.0.0' to listen on all -# available network interfaces. -#host = 127.0.0.1 - -# Use a threadpool for the web server instead of creating a thread for each -# request. -use_threadpool = True - -# Number of threads in the web server thread pool. -#threadpool_workers = 10 - -# ---- Filters -------------------------------------------------------------- - -# Filters sit between Galaxy and the HTTP server. - -# These filters are disabled by default. They can be enabled with -# 'filter-with' in the [app:main] section below. - -# Define the gzip filter. -[filter:gzip] -use = egg:Paste#gzip - -# Define the proxy-prefix filter. -[filter:proxy-prefix] -use = egg:PasteDeploy#prefix -prefix = /galaxy - -# ---- Galaxy --------------------------------------------------------------- - -# Configuration of the Galaxy application. - -[app:main] - -# -- Application and filtering - -# The factory for the WSGI application. This should not be changed. -paste.app_factory = galaxy.web.buildapp:app_factory - -# If not running behind a proxy server, you may want to enable gzip compression -# to decrease the size of data transferred over the network. If using a proxy -# server, please enable gzip compression there instead. -#filter-with = gzip - -# If running behind a proxy server and Galaxy is served from a subdirectory, -# enable the proxy-prefix filter and set the prefix in the -# [filter:proxy-prefix] section above. -#filter-with = proxy-prefix - -# If proxy-prefix is enabled and you're running more than one Galaxy instance -# behind one hostname, you will want to set this to the same 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 = None - -# -- Database - -# By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You -# may use a SQLAlchemy connection string to specify an external database -# instead. This string takes many options which are explained in detail in the -# config file documentation. -#database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE - -# If the server logs errors about not having enough database pool connections, -# you will want to increase these values, or consider running more Galaxy -# processes. -#database_engine_option_pool_size = 5 -#database_engine_option_max_overflow = 10 - -# If using MySQL and the server logs the error "MySQL server has gone away", -# you will want to set this to some positive value (7200 should work). -#database_engine_option_pool_recycle = -1 - -# If large database query results are causing memory or response time issues in -# the Galaxy process, leave the result on the server instead. This option is -# only available for PostgreSQL and is highly recommended. -#database_engine_option_server_side_cursors = False - -# Create only one connection to the database per thread, to reduce the -# connection overhead. Recommended when not using SQLite: -#database_engine_option_strategy = threadlocal - -# Log all database transactions, can be useful for debugging and performance -# profiling. Logging is done via Python's 'logging' module under the qualname -# 'galaxy.model.orm.logging_connection_proxy' -#database_query_profiling_proxy = False - -# -- Files and directories - -# Path where genome builds are stored. This defaults to tool-data/genome -#genome_data_path = tool-data/genome - -# URL for rsync server to download pre-built indexes. -#rsync_url = rsync://scofield.bx.psu.edu/indexes - -# Dataset files are stored in this directory. -#file_path = database/files - -# Temporary files are stored in this directory. -#new_file_path = database/tmp - -# Tool config files, defines what tools are available in Galaxy. -# Tools can be locally developed or installed from Galaxy tool sheds. -#tool_config_file = tool_conf.xml,shed_tool_conf.xml - -# Default path to the directory containing the tools defined in tool_conf.xml. -# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. -#tool_path = tools - -# Path to the directory in which managed tool dependencies are placed. To use -# the dependency system, see the documentation at: -# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies -#tool_dependency_dir = None - -# Enable automatic polling of relative tool sheds to see if any updates -# are available for installed repositories. Ideally only one Galaxy -# server process should be able to check for repository updates. The -# setting for hours_between_check should be an integer between 1 and 24. -#enable_tool_shed_check = False -#hours_between_check = 12 - -# Directory where data used by tools is located, see the samples in that -# directory and the wiki for help: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration -#tool_data_path = tool-data - -# Directory where chrom len files are kept, currently mainly used by trackster -#len_file_path = tool-data/shared/ucsc/chrom - -# Datatypes config file, defines what data (file) types are available in -# Galaxy. -#datatypes_config_file = datatypes_conf.xml - -# Each job is given a unique empty directory as its current working directory. -# This option defines in what parent directory those directories will be -# created. -#job_working_directory = database/job_working_directory - -# If using a cluster, Galaxy will write job scripts and stdout/stderr to this -# directory. -#cluster_files_directory = database/pbs - -# External service types config file, defines what types of external_services configurations -# are available in Galaxy. -#external_service_type_config_file = external_service_types_conf.xml - -# Path to the directory containing the external_service_types defined in the config. -#external_service_type_path = external_service_types - -# Tools with a number of outputs not known until runtime can write these -# outputs to a directory for collection by Galaxy when the job is done. -# Previously, this directory was new_file_path, but using one global directory -# can cause performance problems, so using job_working_directory ('.' or cwd -# when a job is run) is encouraged. By default, both are checked to avoid -# breaking existing tools. -#collect_outputs_from = new_file_path,job_working_directory - -# -- Mail and notification - -# Galaxy sends mail for various things: Subscribing users to the mailing list -# if they request it, emailing password resets, notification from the Galaxy -# Sample Tracking system, and reporting dataset errors. To do this, it needs -# to send mail through an SMTP server, which you may define here (host:port). -# Galaxy will automatically try STARTTLS but will continue upon failure. -#smtp_server = None - -# 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 = None -#smtp_password = None - -# On the user registration form, users may choose to join the mailing list. -# This is the address of the list they'll be subscribed to. -#mailing_join_addr = galaxy-announce-join@bx.psu.edu - -# Datasets in an error state include a link to report the error. Those reports -# will be sent to this address. Error reports are disabled if no address is set. -#error_email_to = None - -# -- Display sites - -# Galaxy can display data at various external browsers. These options specify -# which browsers should be available. URLs and builds available at these -# browsers are defined in the specifield files. - -# UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt -#ucsc_display_sites = main,test,archaea,ucla - -# GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt -#gbrowse_display_sites = modencode,sgd_yeast,tair,wormbase,wormbase_ws120,wormbase_ws140,wormbase_ws170,wormbase_ws180,wormbase_ws190,wormbase_ws200,wormbase_ws204,wormbase_ws210,wormbase_ws220,wormbase_ws225 - -# GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt -#genetrack_display_sites = main,test - -# If use_remote_user = True, display application servers will be denied access -# to Galaxy and so displaying datasets in these sites will fail. -# display_servers contains a list of hostnames which should be allowed to -# bypass security to display datasets. Please be aware that there are security -# implications if this is allowed. More details (including required changes to -# the proxy server config) are available in the Apache proxy documentation on -# the wiki. -# -# The list of servers in this sample config are for the UCSC Main, Test and -# Archaea browsers, but the default if left commented is to not allow any -# display sites to bypass security (you must uncomment the line below to allow -# them). -#display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw5.cse.ucsc.edu,hgw6.cse.ucsc.edu,hgw7.cse.ucsc.edu,hgw8.cse.ucsc.edu,lowepub.cse.ucsc.edu - -# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. - -use_nglims = False -nglims_config_file = tool-data/nglims.yaml - -# -- UI Localization - -# Append "/{brand}" to the "Galaxy" text in the masthead. -#brand = None - -# The URL linked by the "Galaxy/brand" text. -#logo_url = / - -# The URL linked by the "Galaxy Wiki" link in the "Help" menu. -#wiki_url = http://wiki.g2.bx.psu.edu/ - -# The URL linked by the "Support" link in the "Help" menu. -#support_url = http://wiki.g2.bx.psu.edu/Support - -# The URL linked by the "How to Cite..." link in the "Help" menu. -#citation_url = http://wiki.g2.bx.psu.edu/Citing%20Galaxy - -# The URL linked by the "Terms and Conditions" link in the "Help" menu, as well -# as on the user registration and login forms. -#terms_url = None - -# The URL linked by the "Galaxy Q&A" link in the "Help" menu -qa_url = http://slyfox.bx.psu.edu:8080/ - -# Serve static content, which must be enabled if you're not serving it via a -# proxy server. These options should be self explanatory and so are not -# documented individually. You can use these paths (or ones in the proxy -# server) to point to your own styles. -static_enabled = True -static_cache_time = 360 -static_dir = %(here)s/static/ -static_images_dir = %(here)s/static/images -static_favicon_dir = %(here)s/static/favicon.ico -static_scripts_dir = %(here)s/static/scripts/ -static_style_dir = %(here)s/static/june_2007_style/blue -static_robots_txt = %(here)s/static/robots.txt - -# Pack javascript at launch (/static/scripts/*.js) -# This only happens if the modified timestamp of the source .js is newer -# than the version (if it exists) in /static/scripts/packed/ -# Note that this requires java > 1.4 for executing yuicompressor.jar -#pack_scripts = False - -# Enable Cloud Launch - -#enable_cloud_launch = False - -# -- Advanced proxy features - -# For help on configuring the Advanced proxy features, see: -# http://usegalaxy.org/production - -# Apache can handle file downloads (Galaxy-to-user) via mod_xsendfile. Set -# this to True to inform Galaxy that mod_xsendfile is enabled upstream. -#apache_xsendfile = False - -# The same download handling can be done by nginx using X-Accel-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 = False - -# nginx can make use of mod_zip to create zip files containing multiple library -# files. If using X-Accel-Redirect, this can be the same value as that option. -#nginx_x_archive_files_base = False - -# If using compression in the upstream proxy server, use this option to disable -# gzipping of library .tar.gz and .zip archives, since the proxy server will do -# it faster on the fly. -#upstream_gzip = False - -# nginx can also handle file uploads (user-to-Galaxy) via nginx_upload_module. -# Configuration for this is complex and explained 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 = False - -# 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 = False - -# -- Logging and Debugging - -# Verbosity of console log messages. Acceptable values can be found here: -# http://docs.python.org/library/logging.html#logging-levels -#log_level = DEBUG - -# Print database operations to the server log (warning, quite verbose!). -#database_engine_option_echo = False - -# Print database pool operations to the server log (warning, quite verbose!). -#database_engine_option_echo_pool = False - -# Turn on logging of application events and some user events to the database. -#log_events = True - -# Turn on logging of user actions to the database. Actions currently logged are -# grid views, tool searches, and use of "recently" used tools menu. The -# log_events and log_actions functionality will eventually be merged. -#log_actions = True - -# Sanitize All HTML Tool Output -# By default, all tool output served as 'text/html' will be sanitized -# thoroughly. This can be disabled if you have special tools that require -# unaltered output. -#sanitize_all_html = True - -# Debug enables access to various config options useful for development and -# debugging: use_lint, use_profile, use_printdebug and use_interactive. It -# also causes the files used by PBS/SGE (submission script, output, and error) -# to remain on disk after the job is complete. Debug mode is disabled if -# commented, but is uncommented by default in the sample config. -debug = True - -# Check for WSGI compliance. -#use_lint = False - -# Run the Python profiler on each request. -#use_profile = False - -# Intercept print statements and show them on the returned page. -#use_printdebug = True - -# Enable live debugging in your browser. This should NEVER be enabled on a -# public site. Enabled in the sample config for development. -use_interactive = True - -# Write thread status periodically to 'heartbeat.log', (careful, uses disk -# space rapidly!). Useful to determine why your processes may be consuming a -# lot of CPU. -#use_heartbeat = False - -# Enable the memory debugging interface (careful, negatively impacts server -# performance). -#use_memdump = False - -# -- Data Libraries - -# These library upload options are described in much more detail in the wiki: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files - -# Add an option to the library upload form which allows administrators to -# upload a directory of files. -#library_import_dir = None - -# 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 = None - -# Add an option to the admin library upload tool allowing admins to paste -# filesystem paths to files and directories in a box, and these paths will be -# added to a library. Set to True to enable. Please note the security -# implication that this will give Galaxy Admins access to anything your Galaxy -# user has access to. -#allow_library_path_paste = False - -# Users may choose to download multiple files from a library in an archive. By -# default, Galaxy allows users to select from a few different archive formats -# if testing shows that Galaxy is able to create files using these formats. -# Specific formats can be disabled with this option, separate more than one -# format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. -#disable_library_comptypes = - -# Some sequencer integration features in beta allow you to automatically -# transfer datasets. This is done using a lightweight transfer manager which -# runs outside of Galaxy (but is spawned by it automatically). Galaxy will -# communicate with this manager over the port specified here. -#transfer_manager_port = 8163 - -# Search data libraries with whoosh -#enable_whoosh_library_search = True -# Whoosh indexes are stored in this directory. -#whoosh_index_dir = database/whoosh_indexes - -# Search data libraries with lucene -#enable_lucene_library_search = False -# maxiumum file size to index for searching, in MB -#fulltext_max_size = 500 -#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger -# base URL of server providing search functionality using lucene -#fulltext_url = http://localhost:8081 - -# -- Users and Security - -# Galaxy encodes various internal values when these values will be output in -# some format (for example, in a URL or cookie). You should set a key to be -# used by the algorithm that encodes and decodes these values. It can be any -# string. If left unchanged, anyone could construct a cookie that would grant -# them access to others' sessions. -#id_secret = USING THE DEFAULT IS NOT SECURE! - -# User authentication can be delegated to an upstream proxy server (usually -# Apache). The upstream proxy should set a REMOTE_USER header in the request. -# Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy -#use_remote_user = False - -# If use_remote_user is enabled and your external authentication -# 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 = None - -# If use_remote_user is enabled, you can set this to a URL that will log your -# users out. -#remote_user_logout_href = None - -# Administrative users - set this to a comma-separated list of valid Galaxy -# users (email addresses). These users will have access to the Admin section -# of the server, and will have access to create users, groups, roles, -# libraries, and more. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Interface -#admin_users = None - -# Force everyone to log in (disable anonymous access). -#require_login = False - -# Allow unregistered users to create new accounts (otherwise, they will have to -# be created by an admin). -#allow_user_creation = True - -# Allow administrators to delete accounts. -#allow_user_deletion = False - -# Allow administrators to log in as other users (useful for debugging) -#allow_user_impersonation = False - -# Allow users to remove their datasets from disk immediately (otherwise, -# datasets will be removed after a time period specified by an administrator in -# the cleanup scripts run via cron) -#allow_user_dataset_purge = False - -# By default, users' data will be public, but setting this to True will cause -# it to be private. Does not affect existing users and data, only ones created -# after this option is set. Users may still change their default back to -# public. -#new_user_dataset_access_role_default_private = False - -# -- Beta features - -# Object store mode (valid options are: disk, s3, swift, distributed, hierarchical) -#object_store = disk -#os_access_key = <your cloud object store access key> -#os_secret_key = <your cloud object store secret key> -#os_bucket_name = <name of an existing object store bucket or container> -# If using 'swift' object store, you must specify the following connection properties -#os_host = swift.rc.nectar.org.au -#os_port = 8888 -#os_is_secure = False -#os_conn_path = / -# Reduced redundancy can be used only with the 's3' object store -#os_use_reduced_redundancy = False -# Size (in GB) that the cache used by object store should be limited to. -# If the value is not specified, the cache size will be limited only by the -# file system size. The file system location of the cache is considered the -# configuration of the ``file_path`` directive defined above. -#object_store_cache_size = 100 - -# Configuration file for the distributed object store, if object_store = -# distributed. See the sample at distributed_object_store_conf.xml.sample -#distributed_object_store_config_file = None - -# Enable Galaxy to communicate directly with a sequencer -#enable_sequencer_communication = False - -# Enable authentication via OpenID. Allows users to log in to their Galaxy -# account by authenticating with an OpenID provider. -#enable_openid = False -#openid_config_file = openid_conf.xml - -# Optional list of email addresses of API users who can make calls on behalf of -# other users -#api_allow_run_as = None - -# Enable tool tags (associating tools with tags). This has its own option -# since its implementation has a few performance implications on startup for -# large servers. -#enable_tool_tags = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# The URL to the myExperiment instance being used (omit scheme but include port) -#myexperiment_url = www.myexperiment.org:80 - -# Enable Galaxy's "Upload via FTP" interface. You'll need to install and -# configure an FTP server (we've used ProFTPd since it can use Galaxy's -# database for authentication) and set the following two options. - -# This should point to a directory containing subdirectories matching users' -# email addresses, where Galaxy will look for files. -#ftp_upload_dir = None - -# This should be the hostname of your FTP server, which will be provided to -# users in the help text. -#ftp_upload_site = None - -# Enable enforcement of quotas. Quotas can be set from the Admin interface. -#enable_quotas = False - -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - -# -- Job Execution - -# To increase performance of job execution and the web interface, you can -# separate Galaxy into multiple processes. There are more than one way to do -# this, and they are explained in detail in the documentation: -# -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scali... -# -# By default, Galaxy manages and executes jobs from within a single process and -# notifies itself of new jobs via in-memory queues. If you change job_manager -# and job_handlers from their default values, notification will instead be done -# using the `state` and `handler` columns of the job table in the database. - -# Identify the server_name (the string following server: at the top of this -# file) which should be designated as the job manager (only one): -#job_manager = main - -# Identify the server_name(s) which should be designated as job handlers -# (responsible for starting, tracking, finishing, and cleaning up jobs) as a -# comma-separated list. -#job_handlers = main - -# By default, a handler from job_handlers will be selected at random if the -# tool to run does specify a handler below in [galaxy:tool_handlers]. If you -# want certain handlers to only handle jobs for tools/params explicitly -# assigned below, use default_job_handlers to specify which handlers should be -# used for jobs without explicit handlers. -#default_job_handlers = main - -# This enables splitting of jobs into tasks, if specified by the particular tool config. -# This is a new feature and not recommended for production servers yet. -#use_tasked_jobs = False -#local_task_queue_workers = 2 - -# Enable job recovery (if Galaxy is restarted while cluster jobs are running, -# it can "recover" them when it starts). This is not safe to use if you are -# running more than one Galaxy server using the same database. -#enable_job_recovery = True - -# Setting metadata on job outputs to in a separate process (or if using a -# cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the -# hefty expense that setting metadata incurs, your Galaxy process may become -# unresponsive when this operation occurs internally. -#set_metadata_externally = False - -# Although it is fairly reliable, setting metadata can occasionally fail. In -# these instances, you can choose to retry setting it internally or leave it in -# a failed state (since retrying internally may cause the Galaxy process to be -# unresponsive). If this option is set to False, the user will be given the -# option to retry externally, or set metadata manually (when possible). -#retry_metadata_internally = True - -# If (for example) you run on a cluster and your datasets (by default, -# database/files/) are mounted read-only, this option will override tool output -# paths to write outputs to the working directory instead, and the job manager -# will move the outputs to their proper place in the dataset directory on the -# Galaxy server after the job completes. -#outputs_to_working_directory = False - -# If your network filesystem's caching prevents the Galaxy server from seeing -# the job's stdout and stderr files when it completes, you can retry reading -# these files. The job runner will retry the number of times specified below, -# waiting 1 second between tries. For NFS, you may want to try the -noac mount -# option (Linux) or -actimeo=0 (Solaris). -#retry_job_output_collection = 0 - -# Clean up various bits of jobs left on the filesystem after completion. These -# bits include the job working directory, external metadata temporary files, -# and DRM stdout and stderr files (if using a DRM). Possible values are: -# always, onsuccess, never -#cleanup_job = always - -# Number of concurrent jobs to run (local job runner) -#local_job_queue_workers = 5 - -# Jobs can be killed after a certain amount of execution time. Format is in -# hh:mm:ss. Currently only implemented for PBS. -#job_walltime = None - -# Jobs can be killed if any of their outputs grow over a certain size (in -# bytes). 0 for no limit. -#output_size_limit = 0 - -# Jobs can be held back from submission to a runner if a user already has more -# jobs queued or running than the number specified below. This prevents a -# single user from stuffing the queue and preventing other users from being -# able to run jobs. -#user_job_limit = None - -# Clustering Galaxy is not a straightforward process and requires some -# pre-configuration. See the the wiki before attempting to set any of these -# options: -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster - -# Comma-separated list of job runners to start. local is always started. If -# left commented, no jobs will be run on the cluster, even if a cluster URL is -# explicitly defined in the [galaxy:tool_runners] section below. The runners -# currently available are 'pbs' and 'drmaa'. -#start_job_runners = None - -# For sites where all users in Galaxy match users on the system on which Galaxy -# runs, the DRMAA job runner can be configured to submit jobs to the DRM as the -# actual user instead of as the user running the Galaxy server process. For -# details on these options, see the documentation at: -# -# http://galaxyproject.org/wiki/Admin/Config/Performance/Cluster -# -#drmaa_external_runjob_script = scripts/drmaa_external_runner.py -#drmaa_external_killjob_script = scripts/drmaa_external_killer.py -#external_chown_script = scripts/external_chown_script.py - -# File to source to set up the environment when running jobs. By default, the -# environment in which the Galaxy server starts is used when running jobs -# locally, and the environment set up per the DRM's submission method and -# policy is used when running jobs on a cluster (try testing with `qsub` on the -# command line). environment_setup_file can be set to the path of a file on -# the cluster that should be sourced by the user to set up the environment -# 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. This only affects cluster jobs, not local jobs. -#environment_setup_file = None - -# The URL for the default runner to use when a tool doesn't explicitly define a -# runner below. -#default_cluster_job_runner = local:/// - -# The cluster runners have their own thread pools used to prepare and finish -# jobs (so that these sometimes lengthy operations do not block normal queue -# operation). The value here is the number of worker threads available to each -# started runner. -#cluster_job_queue_workers = 3 - -# These options are only used when using file staging with PBS. -#pbs_application_server = -#pbs_stage_path = -#pbs_dataset_server = - -# This option allows users to see the full path of datasets via the "View -# Details" option in the history. Administrators can always see this. -#expose_dataset_path = False - -# ---- Per-Tool Job Management ---------------------------------------------- - -# Per-tool job handler and runner overrides. Parameters can be included to define multiple -# runners per tool. E.g. to run Cufflinks jobs initiated from Trackster -# differently than standard Cufflinks jobs: -# -# cufflinks = local:/// -# cufflinks[source@trackster] = local:/// - -[galaxy:tool_handlers] - -# By default, Galaxy will select a handler at random from the list of -# job_handlers set above. You can override as in the following examples: -# -#upload1 = upload_handler -#cufflinks[source@trackster] = realtime_handler - -[galaxy:tool_runners] - -# If not listed here, a tool will run with the runner defined with -# default_cluster_job_runner. These overrides for local:/// are done because -# these tools can fetch data from remote sites, which may not be suitable to -# run on a cluster (if it does not have access to the Internet, for example). - -biomart = local:/// -encode_db1 = local:/// -hbvar = local:/// -microbial_import1 = local:/// -ucsc_table_direct1 = local:/// -ucsc_table_direct_archaea1 = local:/// -ucsc_table_direct_test1 = local:/// -upload1 = local:/// - -# ---- Galaxy Message Queue ------------------------------------------------- - -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. - -[galaxy_amqp] - -#host = 127.0.0.1 -#port = 5672 -#userid = galaxy -#password = galaxy -#virtual_host = galaxy_messaging_engine -#queue = galaxy_queue -#exchange = galaxy_exchange -#routing_key = bar_code_scanner -#rabbitmqctl_path = /path/to/rabbitmqctl -

diff -r 95d98a26518349216a335a5860eb370ab74375fd -r 1a56c4b28c6bbaf1b2f1b0efec5fecce7bd454bb universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -263,6 +263,9 @@ # as on the user registration and login forms. #terms_url = None

+# The URL linked by the "Galaxy Q&A" link in the "Help" menu +qa_url = http://slyfox.bx.psu.edu:8080/ + # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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