1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/95d98a265183/ changeset: 95d98a265183 user: rmarenco date: 2012-09-07 02:55:35 summary: When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in unverse affected #: 3 files

diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd database/compiled_templates/webapps/galaxy/base_panels.mako.py --- /dev/null +++ b/database/compiled_templates/webapps/galaxy/base_panels.mako.py @@ -0,0 +1,415 @@ +# -*- 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 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd templates/tool_form.mako --- a/templates/tool_form.mako +++ b/templates/tool_form.mako @@ -302,8 +302,8 @@ ${tool.name} ${tool_version_select_field.get_html()} %endif <!-- BioStar links --> - <a href="http://slyfox.bx.psu.edu:8081/new/post/" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> - <a href="http://slyfox.bx.psu.edu:8081/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a> + <a href="http://slyfox.bx.psu.edu:8080/new/post/tagged/${low_tool_name}" target="galaxy_main" class="icon-button general-question tooltip close-side-panels" data-original-title="Ask a tool related question"></a> + <a href="http://slyfox.bx.psu.edu:8080/show/tag/${low_tool_name}/" target="galaxy_main" class="icon-button tag-question tooltip close-side-panels" data-original-title="See tool related posts" ></a><!-- End of BioStar links --></div><div class="toolFormBody">

diff -r 2f684dfa8d474560f241388bbb1fec5c612eca75 -r 95d98a26518349216a335a5860eb370ab74375fd universe_wsgi.ini --- /dev/null +++ b/universe_wsgi.ini @@ -0,0 +1,753 @@ +# +# 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 +

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