March 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Remove print debug.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2b27b1e42fc9/ changeset: 2b27b1e42fc9 user: dan date: 2012-03-24 01:50:32 summary: Remove print debug. affected #: 1 file diff -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 -r 2b27b1e42fc90c4077c9ddcb963612efab28d940 lib/galaxy/openid/providers.py --- a/lib/galaxy/openid/providers.py +++ b/lib/galaxy/openid/providers.py @@ -76,7 +76,6 @@ for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): if store_pref_value_name in ( self.sreg_optional + self.sreg_required ): trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name ) - print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ] else: raise Exception( 'Only sreg is currently supported.' ) trans.sa_session.add( trans.user ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b9e188c4ecba/ changeset: b9e188c4ecba user: dan date: 2012-03-23 18:41:01 summary: Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed. affected #: 17 files diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -13,6 +13,7 @@ from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.tools.imp_exp import load_history_imp_exp_tools from galaxy.sample_tracking import external_service_types +from galaxy.openid.providers import OpenIDProviders class UniverseApplication( object ): """Encapsulates the state of a Universe application""" @@ -105,6 +106,9 @@ if self.config.enable_openid: from galaxy.web.framework import openid_manager self.openid_manager = openid_manager.OpenIDManager( self.config.openid_consumer_cache_path ) + self.openid_providers = OpenIDProviders.from_file( self.config.openid_config ) + else: + self.openid_providers = OpenIDProviders() # Start the heartbeat process if configured and available if self.config.use_heartbeat: from galaxy.util import heartbeat diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -44,7 +44,9 @@ self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) + # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) + self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) self.tool_sheds_config = kwargs.get( 'tool_sheds_config_file', 'tool_sheds_conf.xml' ) self.enable_unique_workflow_defaults = string_as_bool( kwargs.get( 'enable_unique_workflow_defaults', False ) ) diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/openid/__init__.py --- /dev/null +++ b/lib/galaxy/openid/__init__.py @@ -0,0 +1,3 @@ +""" +OpenID functionality +""" \ No newline at end of file diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/openid/providers.py --- /dev/null +++ b/lib/galaxy/openid/providers.py @@ -0,0 +1,118 @@ +""" +Contains OpenID provider functionality +""" + +import logging, os +from galaxy.util import parse_xml, string_as_bool +from galaxy.util.odict import odict + + +log = logging.getLogger( __name__ ) + +class OpenIDProvider( object ): + '''An OpenID Provider object.''' + @classmethod + def from_file( cls, filename ): + return cls.from_elem( parse_xml( filename ).getroot() ) + @classmethod + def from_elem( cls, xml_root ): + provider_elem = xml_root + provider_id = provider_elem.get( 'id', None ) + provider_name = provider_elem.get( 'name', provider_id ) + op_endpoint_url = provider_elem.find( 'op_endpoint_url' ) + if op_endpoint_url is not None: + op_endpoint_url = op_endpoint_url.text + assert (provider_id and provider_name and op_endpoint_url), Exception( "OpenID Provider improperly configured" ) + sreg_required = [] + sreg_optional = [] + use_for = {} + store_user_preference = {} + use_default_sreg = True + for elem in provider_elem.findall( 'sreg' ): + use_default_sreg = False + for field_elem in elem.findall( 'field' ): + sreg_name = field_elem.get( 'name' ) + assert sreg_name, Exception( 'A name is required for a sreg element' ) + if string_as_bool( field_elem.get( 'required' ) ): + sreg_required.append( sreg_name ) + else: + sreg_optional.append( sreg_name ) + for use_elem in field_elem.findall( 'use_for' ): + use_for[ use_elem.get( 'name' ) ] = sreg_name + for store_user_preference_elem in field_elem.findall( 'store_user_preference' ): + store_user_preference[ store_user_preference_elem.get( 'name' ) ] = sreg_name + if use_default_sreg: + sreg_required = None + sreg_optional = None + use_for = None + return cls( provider_id, provider_name, op_endpoint_url, sreg_required, sreg_optional, use_for, store_user_preference ) + def __init__( self, id, name, op_endpoint_url, sreg_required=None, sreg_optional=None, use_for=None, store_user_preference=None ): + '''When sreg options are not specified, defaults are used.''' + self.id = id + self.name = name + self.op_endpoint_url = op_endpoint_url + if sreg_optional is None: + self.sreg_optional = [ 'nickname', 'email' ] + else: + self.sreg_optional = sreg_optional + if sreg_required: + self.sreg_required = sreg_required + else: + self.sreg_required = [] + if use_for is not None: + self.use_for = use_for + else: + self.use_for = {} + if 'nickname' in ( self.sreg_optional + self.sreg_required ): + self.use_for[ 'username' ] = 'nickname' + if 'email' in ( self.sreg_optional + self.sreg_required ): + self.use_for[ 'email' ] = 'email' + if store_user_preference: + self.store_user_preference = store_user_preference + else: + self.store_user_preference = {} + def post_authentication( self, trans, openid_manager, info ): + sreg_attributes = openid_manager.get_sreg( info ) + for store_pref_name, store_pref_value_name in self.store_user_preference.iteritems(): + if store_pref_value_name in ( self.sreg_optional + self.sreg_required ): + trans.user.preferences[ store_pref_name ] = sreg_attributes.get( store_pref_value_name ) + print 'setting',store_pref_name,'to',trans.user.preferences[ store_pref_name ] + else: + raise Exception( 'Only sreg is currently supported.' ) + trans.sa_session.add( trans.user ) + trans.sa_session.flush() + +class OpenIDProviders( object ): + '''Collection of OpenID Providers''' + @classmethod + def from_file( cls, filename ): + try: + return cls.from_elem( parse_xml( filename ).getroot() ) + except Exception, e: + log.error( 'Failed to load OpenID Providers: %s' % ( e ) ) + return cls() + @classmethod + def from_elem( cls, xml_root ): + oid_elem = xml_root + providers = odict() + for elem in oid_elem.findall( 'provider' ): + try: + provider = OpenIDProvider.from_file( os.path.join( 'openid', elem.get( 'file' ) ) ) + providers[ provider.id ] = provider + log.debug( 'Loaded OpenID provider: %s (%s)' % ( provider.name, provider.id ) ) + except Exception, e: + log.error( 'Failed to add OpenID provider: %s' % ( e ) ) + return cls( providers ) + def __init__( self, providers=None ): + if providers: + self.providers = providers + else: + self.providers = odict() + def __iter__( self ): + for provider in self.providers.itervalues(): + yield provider + def get( self, name, default=None ): + if name in self.providers: + return self.providers[ name ] + else: + return default diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -11,6 +11,7 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.web.framework.helpers import iff from galaxy.security.validate_user_input import validate_email, validate_publicname, validate_password +from galaxy.openid.providers import OpenIDProvider log = logging.getLogger( __name__ ) @@ -21,12 +22,6 @@ <p/> """ -OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', - 'Yahoo!' : 'http://yahoo.com', - 'AOL/AIM' : 'http://openid.aol.com', - 'Launchpad' : 'http://login.launchpad.net', - } - class UserOpenIDGrid( grids.Grid ): use_panels = False title = "OpenIDs linked to your account" @@ -68,19 +63,26 @@ if not referer: referer = url_for( '/' ) consumer = trans.app.openid_manager.get_consumer( trans ) - process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate ) - if not openid_url and openid_provider and openid_provider in OPENID_PROVIDERS: - openid_url = OPENID_PROVIDERS[openid_provider] - if openid_url: + openid_provider_obj = None + if not openid_url and openid_provider and trans.app.openid_providers.get( openid_provider ): + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + elif openid_url: + openid_provider_obj = OpenIDProvider( openid_url, openid_url, openid_url ) #for manually entered links use the link for id, name and url + elif openid_provider: + message = 'Invalid OpenID provider specified: %s' % ( openid_provider ) + else: + message = 'An OpenID provider was not specified' + process_url = trans.request.base.rstrip( '/' ) + url_for( controller='user', action='openid_process', referer=referer, auto_associate=auto_associate, openid_provider=openid_provider ) + if openid_provider_obj is not None: request = None try: - request = consumer.begin( openid_url ) + request = consumer.begin( openid_provider_obj.op_endpoint_url ) if request is None: - message = 'No OpenID services are available at %s' % openid_url + message = 'No OpenID services are available at %s' % openid_provider_obj.op_endpoint_url except Exception, e: message = 'Failed to begin OpenID authentication: %s' % str( e ) if request is not None: - trans.app.openid_manager.add_sreg( trans, request, optional=[ 'nickname', 'email' ] ) + sreg_request = trans.app.openid_manager.add_sreg( trans, request, required=openid_provider_obj.sreg_required, optional=openid_provider_obj.sreg_optional ) if request.shouldSendRedirect(): redirect_url = request.redirectURL( trans.request.base, process_url ) @@ -114,6 +116,7 @@ info = consumer.complete( kwd, trans.request.url ) display_identifier = info.getDisplayIdentifier() redirect_url = kwd.get( 'referer', url_for( '/' ) ) + openid_provider = kwd.get( 'openid_provider', '' ) if info.status == trans.app.openid_manager.FAILURE and display_identifier: message = "Login via OpenID failed. The technical reason for this follows, please include this message in your email if you need to %s to resolve this problem: %s" % ( contact, info.message ) return trans.response.send_redirect( url_for( controller='user', @@ -125,6 +128,9 @@ if info.endpoint.canonicalID: display_identifier = info.endpoint.canonicalID user_openid = trans.sa_session.query( trans.app.model.UserOpenID ).filter( trans.app.model.UserOpenID.table.c.openid == display_identifier ).first() + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) + if not openid_provider_obj: + openid_provider_obj = OpenIDProvider( display_identifier, display_identifier, display_identifier ) if not user_openid: user_openid = trans.app.model.UserOpenID( session=trans.galaxy_session, openid=display_identifier ) elif not user_openid.user and user_openid.session.id != trans.galaxy_session.id: @@ -132,6 +138,7 @@ elif user_openid.user and not auto_associate: trans.handle_user_login( user_openid.user, webapp ) trans.log_event( "User logged in via OpenID: %s" % display_identifier ) + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) trans.response.send_redirect( redirect_url ) return if auto_associate and trans.user: @@ -151,6 +158,7 @@ trans.log_event( "User associated OpenID: %s" % display_identifier ) message = "The OpenID <strong>%s</strong> has been associated with your Galaxy account, <strong>%s</strong>." % ( display_identifier, trans.user.email ) status = "done" + openid_provider_obj.post_authentication( trans, trans.app.openid_manager, info ) trans.response.send_redirect( url_for( controller='user', action='openid_manage', use_panels=True, @@ -162,15 +170,18 @@ message = "OpenID authentication was successful, but you need to associate your OpenID with a Galaxy account." sreg_resp = trans.app.openid_manager.get_sreg( info ) try: - username = sreg_resp.get( 'nickname', '' ) + sreg_username_name = openid_provider_obj.use_for.get( 'username' ) + username = sreg_resp.get( sreg_username_name, '' ) except AttributeError: username = '' try: - email = sreg_resp.get( 'email', '' ) + sreg_email_name = openid_provider_obj.use_for.get( 'email' ) + email = sreg_resp.get( sreg_email_name, '' ) except AttributeError: email = '' trans.response.send_redirect( url_for( controller='user', action='openid_associate', + openid_provider=openid_provider, use_panels=True, username=username, email=email, @@ -199,6 +210,8 @@ email = kwd.get( 'email', '' ) username = kwd.get( 'username', '' ) referer = kwd.get( 'referer', trans.request.referer ) + openid_provider = kwd.get( 'openid_provider', '' ) + openid_provider_obj = trans.app.openid_providers.get( openid_provider ) params = util.Params( kwd ) is_admin = cntrller == 'admin' and trans.user_is_admin() openids = trans.galaxy_session.openids @@ -219,8 +232,9 @@ redirect_url = referer if not redirect_url: redirect_url = url_for( '/' ) - trans.response.send_redirect( redirect_url ) - return + if openid_provider_obj: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) + return trans.response.send_redirect( redirect_url ) if kwd.get( 'create_user_button', False ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) @@ -251,7 +265,9 @@ redirect_url = referer if not redirect_url: redirect_url = url_for( '/' ) - trans.response.send_redirect( redirect_url ) + if openid_provider_obj: + return trans.response.send_redirect( url_for( controller='user', action='openid_auth', openid_provider=openid_provider, referer=redirect_url ) ) + return trans.response.send_redirect( redirect_url ) else: message = error status = 'error' @@ -285,7 +301,8 @@ user_type_fd_id_select_field=user_type_fd_id_select_field, user_type_form_definition=user_type_form_definition, widgets=widgets, - openids=openids ) + openids=openids, + openid_provider=openid_provider ) @web.expose @web.require_login( 'manage OpenIDs' ) def openid_disassociate( self, trans, webapp='galaxy', **kwd ): @@ -340,7 +357,7 @@ use_panels=use_panels, id=kwd['id'] ) ) kwd['referer'] = url_for( controller='user', action='openid_manage', use_panels=True ) - kwd['openid_providers'] = OPENID_PROVIDERS + kwd['openid_providers'] = trans.app.openid_providers return self.user_openid_grid( trans, **kwd ) @web.expose def login( self, trans, webapp='galaxy', redirect_url='', refresh_frames=[], **kwd ): @@ -351,6 +368,7 @@ header = '' user = None email = kwd.get( 'email', '' ) + openid_provider = kwd.get( 'openid_provider', '' ) if kwd.get( 'login_button', False ): if webapp == 'galaxy' and not refresh_frames: if trans.app.config.require_login: @@ -385,7 +403,7 @@ refresh_frames=refresh_frames, message=message, status=status, - openid_providers=OPENID_PROVIDERS, + openid_providers=trans.app.openid_providers, active_view="user" ) def __validate_login( self, trans, webapp='galaxy', **kwd ): message = kwd.get( 'message', '' ) diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 lib/galaxy/web/framework/openid_manager.py --- a/lib/galaxy/web/framework/openid_manager.py +++ b/lib/galaxy/web/framework/openid_manager.py @@ -1,5 +1,5 @@ """ -Mange the OpenID consumer and related data stores. +Manage the OpenID consumer and related data stores. """ import os, pickle, logging diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/aol.xml --- /dev/null +++ b/openid/aol.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="aol" name="AOL/AIM"> + <op_endpoint_url>http://openid.aol.com</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/genomespace.xml --- /dev/null +++ b/openid/genomespace.xml @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<provider id="genomespace" name="GenomeSpace"> + <op_endpoint_url>https://identity.genomespace.org/identityServer/xrd.jsp</op_endpoint_url> + <sreg> + <field name="nickname" required="True"> + <use_for name="username"/> + <store_user_preference name="genomespace_username"/> + </field> + <field name="email" required="False"> + <use_for name="email"/> + </field> + <field name="gender" required="True"> + <store_user_preference name="genomespace_token"/> + </field> + </sreg> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/google.xml --- /dev/null +++ b/openid/google.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="google" name="Google"> + <op_endpoint_url>https://www.google.com/accounts/o8/id</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/launchpad.xml --- /dev/null +++ b/openid/launchpad.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="launchpad" name="Launchpad"> + <op_endpoint_url>http://login.launchpad.net</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid/yahoo.xml --- /dev/null +++ b/openid/yahoo.xml @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<provider id="yahoo" name="Yahoo!"> + <op_endpoint_url>http://yahoo.com</op_endpoint_url> +</provider> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 openid_conf.xml.sample --- /dev/null +++ b/openid_conf.xml.sample @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<openid> + <provider file="google.xml" /> + <provider file="yahoo.xml" /> + <provider file="aol.xml" /> + <provider file="launchpad.xml" /> + <provider file="genomespace.xml" /> +</openid> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 run.sh --- a/run.sh +++ b/run.sh @@ -15,6 +15,7 @@ tool_conf.xml.sample tool_data_table_conf.xml.sample tool_sheds_conf.xml.sample + openid_conf.xml.sample universe_wsgi.ini.sample tool-data/shared/ucsc/builds.txt.sample tool-data/shared/igv/igv_build_sites.txt.sample diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -59,7 +59,7 @@ </%def> -<%def name="render_login_form( form_action=None )"> +<%def name="render_login_form( form_action=None, openid_provider='' )"><% if form_action is None: @@ -77,6 +77,7 @@ <input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/><input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="openid_provider" value="${openid_provider}" /></div><div class="form-row"><label>Password:</label> @@ -94,10 +95,9 @@ </%def><%def name="render_openid_form( referer, auto_associate, openid_providers )"> - <div class="toolForm"><div class="toolFormTitle">OpenID Login</div> - <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" > + <form name="openid" id="openid" action="${h.url_for( controller='user', action='openid_auth' )}" method="post" target="_parent" ><div class="form-row"><label>OpenID URL:</label><input type="text" name="openid_url" size="60" style="background-image:url('${h.url_for( '/static/images/openid-16x16.gif' )}' ); background-repeat: no-repeat; padding-right: 20px; background-position: 99% 50%;"/> @@ -107,8 +107,8 @@ </div><div class="form-row"> Or, authenticate with your <select name="openid_provider"> - %for provider in openid_providers.keys(): - <option>${provider}</option> + %for provider in openid_providers: + <option value="${provider.id}">${provider.name}</option> %endfor </select> account. </div> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -65,11 +65,11 @@ <% form_action = h.url_for( cntrller=cntrller, use_panels=use_panels ) %> - ${render_login_form( form_action=form_action )} + ${render_login_form( form_action=form_action, openid_provider=openid_provider )} <br/> - ${render_registration_form( form_action=form_action )} + ${render_registration_form( form_action=form_action, openid_provider=openid_provider )} </div></div> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 templates/user/register.mako --- a/templates/user/register.mako +++ b/templates/user/register.mako @@ -21,7 +21,7 @@ ${render_registration_form()} %endif -<%def name="render_registration_form( form_action=None )"> +<%def name="render_registration_form( form_action=None, openid_provider='' )"><% if form_action is None: @@ -38,6 +38,7 @@ <input type="text" name="email" value="${email}" size="40"/><input type="hidden" name="webapp" value="${webapp}" size="40"/><input type="hidden" name="referer" value="${referer}" size="40"/> + <input type="hidden" name="openid_provider" value="${openid_provider}" /></div><div class="form-row"><label>Password:</label> diff -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 -r b9e188c4ecba66b5e065ac88b6b9d301a4879156 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -495,6 +495,7 @@ # 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 # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Convert loc file examples to use tabs instead of spaces.
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/463fc935b97c/ changeset: 463fc935b97c user: dannon date: 2012-03-23 13:59:34 summary: Convert loc file examples to use tabs instead of spaces. affected #: 22 files diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/all_fasta.loc.sample --- a/tool-data/all_fasta.loc.sample +++ b/tool-data/all_fasta.loc.sample @@ -4,13 +4,13 @@ #all_fasta.loc. This file has the format (white space characters are #TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, all_fasta.loc could look something like this: # -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb.loc.sample --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -2,7 +2,7 @@ #list of nucleotide BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, @@ -25,9 +25,9 @@ #Your blastdb.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # #See also blastdb_p.loc which is for any protein BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ b/tool-data/blastdb_p.loc.sample @@ -2,25 +2,25 @@ #list of protein BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, #and that the first tab that appears in the line is right before the path. # -#So, for example, if your database is NR and the path to your base name +#So, for example, if your database is NR and the path to your base name #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: # -#nr NCBI NR (non redundant) /data/blastdb/nr +#nr NCBI NR (non redundant) /data/blastdb/nr # #and your /data/blastdb directory would contain all of the files associated #with the database, /data/blastdb/nr.*. # -#Your blastdb_p.loc file should include an entry per line for each "base name" +#Your blastdb_p.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr #...etc... # #See also blastdb.loc which is for any nucleotide BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bowtie_indices_color.loc.sample --- a/tool-data/bowtie_indices_color.loc.sample +++ b/tool-data/bowtie_indices_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bowtie_indices.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, @@ -25,9 +25,9 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index.loc.sample --- a/tool-data/bwa_index.loc.sample +++ b/tool-data/bwa_index.loc.sample @@ -25,10 +25,10 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index_color.loc.sample --- a/tool-data/bwa_index_color.loc.sample +++ b/tool-data/bwa_index_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bwa_index_color.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, for example, if you had phiX indexed stored in #/depot/data2/galaxy/phiX/color/, @@ -25,10 +25,10 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/faseq.loc.sample --- a/tool-data/faseq.loc.sample +++ b/tool-data/faseq.loc.sample @@ -20,7 +20,7 @@ #Your faseq.loc file should include an entry per line for each set of fasta #sequence files you have stored. For example: # -#hg18 /depot/data2/galaxy/faseq/hg18 -#mm9 /depot/data2/galaxy/faseq/mm9 -#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis +#hg18 /depot/data2/galaxy/faseq/hg18 +#mm9 /depot/data2/galaxy/faseq/mm9 +#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gatk_sorted_picard_index.loc.sample --- a/tool-data/gatk_sorted_picard_index.loc.sample +++ b/tool-data/gatk_sorted_picard_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in -#/depot/data2/galaxy/srma/hg18/, +#/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.chrlens.loc.sample --- a/tool-data/gd.chrlens.loc.sample +++ b/tool-data/gd.chrlens.loc.sample @@ -6,17 +6,17 @@ # file has the following format (white space characters are TAB # characters): # -#<species><reference_species_file_path> +#<species><reference_species_file_path> # # So, for example, if you used Monodelphis domestica as the reference # species for a collection of Sarcophilus harrisii SNPs, then the # gd.chrlens.loc entry would look like this: # -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt # # Your gd.chrlens.loc file should include an entry for each pair of # species SNPs and reference species. For example: # -#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.primers.loc.sample --- a/tool-data/gd.primers.loc.sample +++ b/tool-data/gd.primers.loc.sample @@ -5,18 +5,18 @@ # primers files are stored. The gd.primers.loc file has the following # format (white space characters are TAB characters): # -#<species><primers_file_path> +#<species><primers_file_path> # # So, for example, if you had a primers file located at # /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of # Ovis canadensis SNPs, then the gd.primers.loc entry would look like # this: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt # # Your gd.primers.loc file should include an entry for each pair of # species SNPs and primers file. For example: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.snps.loc.sample --- a/tool-data/gd.snps.loc.sample +++ b/tool-data/gd.snps.loc.sample @@ -5,17 +5,17 @@ # SNP call files are stored. The gd.snps.loc file has the following # format (white space characters are TAB characters): # -#<species><SNP_call_file_path> +#<species><SNP_call_file_path> # # So, for example, if you had a SNP call file located at # /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of # Ovis canadensis SNPs, then the gd.snps.loc entry would look like this: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt # # Your gd.snps.loc file should include an entry for each pair of species # SNPs and SNP call file. For example: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/lastz_seqs.loc.sample --- a/tool-data/lastz_seqs.loc.sample +++ b/tool-data/lastz_seqs.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><display_name><file_path> +#<unique_build_id><display_name><file_path> # #So, for example, if your lastz_seqs.loc began like this: # -#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/liftOver.loc.sample --- a/tool-data/liftOver.loc.sample +++ b/tool-data/liftOver.loc.sample @@ -8,7 +8,7 @@ #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, #then the liftOver.loc entry would look like this: # -#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain # #and your /depot/data2/galaxy/anoCar1/liftOver directory would #contain all of your "chain" files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/mosaik_index.loc.sample --- a/tool-data/mosaik_index.loc.sample +++ b/tool-data/mosaik_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The mosaik_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/mosaik/hg18/ #then the mosaik_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa # #and your /depot/data2/galaxy/mosaik/hg18/ directory #would contain the following files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/ngs_sim_fasta.loc.sample --- a/tool-data/ngs_sim_fasta.loc.sample +++ b/tool-data/ngs_sim_fasta.loc.sample @@ -4,17 +4,17 @@ #in this directory) that points to the locations of those files. The ngs_sim.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18chrM.fa in #/data/path/hg18/seq/, #then the ngs_sim.loc entry would look like this: # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa # #Your ngs_sim.loc file should include an entry per line for each FASTA file you #have stored. # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa -#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa -#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa +#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_base_index.loc.sample --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_base_index.loc #file has this format (longer white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_base_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_base_F3_50.index: @@ -21,7 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_color_index.loc.sample --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_color_index.loc #file has this format (white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/picard_index.loc.sample --- a/tool-data/picard_index.loc.sample +++ b/tool-data/picard_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The picard_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/quality_scores.loc.sample --- a/tool-data/quality_scores.loc.sample +++ b/tool-data/quality_scores.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/panTro2/quality_scores, then the quality_scores.loc entry #would look like this: # -#panTro2 /depot/data2/galaxy/panTro2/quality_scores +#panTro2 /depot/data2/galaxy/panTro2/quality_scores # #and your /depot/data2/galaxy/panTro2/quality_scores directory would #contain all of your quality score files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/regions.loc.sample --- a/tool-data/regions.loc.sample +++ b/tool-data/regions.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the #regions.loc entry would look like this: # -#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed +#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed # #and your /depot/data2/galaxy/regions/ directory would #contain all of your regions files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/srma_index.loc.sample --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -8,13 +8,13 @@ #the directories in which those files are stored. The srma_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/, #then the srma_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/twobit.loc.sample --- a/tool-data/twobit.loc.sample +++ b/tool-data/twobit.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/droPer1/, then the twobit.loc entry #would look like this: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit # #and your /depot/data2/galaxy/droPer1/ directory would #contain all of your twobit files (e.g.): @@ -19,8 +19,8 @@ #Your twobit.loc file should include an entry per line for each twobit #file you have stored. For example: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit -#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit -#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit -#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit +#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit +#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit #...etc... Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample
by Bitbucket 23 Mar '12

23 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/732c10115fdf/ changeset: 732c10115fdf user: dannon date: 2012-03-23 13:24:42 summary: =Use tabs instead of spaces for sample lines in bowtie_indices.loc.sample affected #: 1 file diff -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e tool-data/bowtie_indices.loc.sample --- a/tool-data/bowtie_indices.loc.sample +++ b/tool-data/bowtie_indices.loc.sample @@ -7,11 +7,11 @@ # #<unique_build_id><dbkey><display_name><file_base_path> # -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/bowtie/hg18/, +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie/hg18/, #then the bowtie_indices.loc entry would look like this: # -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18 # #and your /depot/data2/galaxy/bowtie/hg18/ directory #would contain hg18.*.ebwt files: @@ -25,9 +25,9 @@ #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove the EMBOSS tools from Main's tool_conf.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1adcc1b43718/ changeset: 1adcc1b43718 user: natefoo date: 2012-03-23 03:16:22 summary: Remove the EMBOSS tools from Main's tool_conf. affected #: 1 file diff -r 9e4fe7f46c621e1b79a33d223b3c9b807135b62c -r 1adcc1b43718a0abc925061fdb6403a60bde2ddb tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -218,115 +218,6 @@ <tool file="genome_diversity/select_restriction_enzymes.xml" /><tool file="genome_diversity/extract_flanking_dna.xml" /></section> - <section name="EMBOSS" id="EMBOSSLite"> - <tool file="emboss_5/emboss_antigenic.xml" /> - <tool file="emboss_5/emboss_backtranseq.xml" /> - <tool file="emboss_5/emboss_banana.xml" /> - <tool file="emboss_5/emboss_biosed.xml" /> - <tool file="emboss_5/emboss_btwisted.xml" /> - <tool file="emboss_5/emboss_cai_custom.xml" /> - <tool file="emboss_5/emboss_cai.xml" /> - <tool file="emboss_5/emboss_chaos.xml" /> - <tool file="emboss_5/emboss_charge.xml" /> - <tool file="emboss_5/emboss_checktrans.xml" /> - <tool file="emboss_5/emboss_chips.xml" /> - <tool file="emboss_5/emboss_cirdna.xml" /> - <tool file="emboss_5/emboss_codcmp.xml" /> - <tool file="emboss_5/emboss_coderet.xml" /> - <tool file="emboss_5/emboss_compseq.xml" /> - <tool file="emboss_5/emboss_cpgplot.xml" /> - <tool file="emboss_5/emboss_cpgreport.xml" /> - <tool file="emboss_5/emboss_cusp.xml" /> - <tool file="emboss_5/emboss_cutseq.xml" /> - <tool file="emboss_5/emboss_dan.xml" /> - <tool file="emboss_5/emboss_degapseq.xml" /> - <tool file="emboss_5/emboss_descseq.xml" /> - <tool file="emboss_5/emboss_diffseq.xml" /> - <tool file="emboss_5/emboss_digest.xml" /> - <tool file="emboss_5/emboss_dotmatcher.xml" /> - <tool file="emboss_5/emboss_dotpath.xml" /> - <tool file="emboss_5/emboss_dottup.xml" /> - <tool file="emboss_5/emboss_dreg.xml" /> - <tool file="emboss_5/emboss_einverted.xml" /> - <tool file="emboss_5/emboss_epestfind.xml" /> - <tool file="emboss_5/emboss_equicktandem.xml" /> - <tool file="emboss_5/emboss_est2genome.xml" /> - <tool file="emboss_5/emboss_etandem.xml" /> - <tool file="emboss_5/emboss_extractfeat.xml" /> - <tool file="emboss_5/emboss_extractseq.xml" /> - <tool file="emboss_5/emboss_freak.xml" /> - <tool file="emboss_5/emboss_fuzznuc.xml" /> - <tool file="emboss_5/emboss_fuzzpro.xml" /> - <tool file="emboss_5/emboss_fuzztran.xml" /> - <tool file="emboss_5/emboss_garnier.xml" /> - <tool file="emboss_5/emboss_geecee.xml" /> - <tool file="emboss_5/emboss_getorf.xml" /> - <tool file="emboss_5/emboss_helixturnhelix.xml" /> - <tool file="emboss_5/emboss_hmoment.xml" /> - <tool file="emboss_5/emboss_iep.xml" /> - <tool file="emboss_5/emboss_infoseq.xml" /> - <tool file="emboss_5/emboss_isochore.xml" /> - <tool file="emboss_5/emboss_lindna.xml" /> - <tool file="emboss_5/emboss_marscan.xml" /> - <tool file="emboss_5/emboss_maskfeat.xml" /> - <tool file="emboss_5/emboss_maskseq.xml" /> - <tool file="emboss_5/emboss_matcher.xml" /> - <tool file="emboss_5/emboss_megamerger.xml" /> - <tool file="emboss_5/emboss_merger.xml" /> - <tool file="emboss_5/emboss_msbar.xml" /> - <tool file="emboss_5/emboss_needle.xml" /> - <tool file="emboss_5/emboss_newcpgreport.xml" /> - <tool file="emboss_5/emboss_newcpgseek.xml" /> - <tool file="emboss_5/emboss_newseq.xml" /> - <tool file="emboss_5/emboss_noreturn.xml" /> - <tool file="emboss_5/emboss_notseq.xml" /> - <tool file="emboss_5/emboss_nthseq.xml" /> - <tool file="emboss_5/emboss_octanol.xml" /> - <tool file="emboss_5/emboss_oddcomp.xml" /> - <tool file="emboss_5/emboss_palindrome.xml" /> - <tool file="emboss_5/emboss_pasteseq.xml" /> - <tool file="emboss_5/emboss_patmatdb.xml" /> - <tool file="emboss_5/emboss_pepcoil.xml" /> - <tool file="emboss_5/emboss_pepinfo.xml" /> - <tool file="emboss_5/emboss_pepnet.xml" /> - <tool file="emboss_5/emboss_pepstats.xml" /> - <tool file="emboss_5/emboss_pepwheel.xml" /> - <tool file="emboss_5/emboss_pepwindow.xml" /> - <tool file="emboss_5/emboss_pepwindowall.xml" /> - <tool file="emboss_5/emboss_plotcon.xml" /> - <tool file="emboss_5/emboss_plotorf.xml" /> - <tool file="emboss_5/emboss_polydot.xml" /> - <tool file="emboss_5/emboss_preg.xml" /> - <tool file="emboss_5/emboss_prettyplot.xml" /> - <tool file="emboss_5/emboss_prettyseq.xml" /> - <tool file="emboss_5/emboss_primersearch.xml" /> - <tool file="emboss_5/emboss_revseq.xml" /> - <tool file="emboss_5/emboss_seqmatchall.xml" /> - <tool file="emboss_5/emboss_seqret.xml" /> - <tool file="emboss_5/emboss_showfeat.xml" /> - <tool file="emboss_5/emboss_shuffleseq.xml" /> - <tool file="emboss_5/emboss_sigcleave.xml" /> - <tool file="emboss_5/emboss_sirna.xml" /> - <tool file="emboss_5/emboss_sixpack.xml" /> - <tool file="emboss_5/emboss_skipseq.xml" /> - <tool file="emboss_5/emboss_splitter.xml" /> - <tool file="emboss_5/emboss_supermatcher.xml" /> - <tool file="emboss_5/emboss_syco.xml" /> - <tool file="emboss_5/emboss_tcode.xml" /> - <tool file="emboss_5/emboss_textsearch.xml" /> - <tool file="emboss_5/emboss_tmap.xml" /> - <tool file="emboss_5/emboss_tranalign.xml" /> - <tool file="emboss_5/emboss_transeq.xml" /> - <tool file="emboss_5/emboss_trimest.xml" /> - <tool file="emboss_5/emboss_trimseq.xml" /> - <tool file="emboss_5/emboss_twofeat.xml" /> - <tool file="emboss_5/emboss_union.xml" /> - <tool file="emboss_5/emboss_vectorstrip.xml" /> - <tool file="emboss_5/emboss_water.xml" /> - <tool file="emboss_5/emboss_wobble.xml" /> - <tool file="emboss_5/emboss_wordcount.xml" /> - <tool file="emboss_5/emboss_wordmatch.xml" /> - </section><label text="NGS Toolbox Beta" id="ngs" /><section name="NGS: QC and manipulation" id="cshl_library_information"><label text="Illumina data" id="illumina" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Pack script.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9e4fe7f46c62/ changeset: 9e4fe7f46c62 user: jgoecks date: 2012-03-23 02:17:09 summary: Pack script. affected #: 1 file diff -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba -r 9e4fe7f46c621e1b79a33d223b3c9b807135b62c static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();console.log(this.$footer,p.buttons);var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").css({background:"white",opacity:0,zIndex:9000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$body.css("min-width",this.$body.width())}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#overlay"),dialog:d("#dialog-box"),backdrop:d("#overlay-background")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+image_path+"/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Reinstate dialog-box class in modal.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b7d0ea8cf233/ changeset: b7d0ea8cf233 user: jgoecks date: 2012-03-22 23:53:55 summary: Reinstate dialog-box class in modal. affected #: 1 file diff -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae -r b7d0ea8cf2334a840b9bef195c06b30e99fcbaba templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -178,7 +178,7 @@ <div id="overlay-background" class="modal-backdrop fade ${overlay_class}"></div> - <div id="dialog-box" class="modal" border="0" ${display}> + <div id="dialog-box" class="modal dialog-box" border="0" ${display}><div class="modal-header"><span><h3 class='title'>${title}</h3></span></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove debugging statement.
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/423d7f6e7b80/ changeset: 423d7f6e7b80 user: jgoecks date: 2012-03-22 23:00:54 summary: Remove debugging statement. affected #: 1 file diff -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 -r 423d7f6e7b80cc294a9324133a49e1cd385c36ae static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -140,7 +140,6 @@ } // Buttons this.$footer.hide(); - console.log( this.$footer, options.buttons ); var $buttons = this.$footer.find( ".buttons" ).html( "" ); if ( options.buttons ) { $.each( options.buttons, function( name, value ) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: fix get_file_peek() to better support datasets with very long lines
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bb19e940a03c/ changeset: bb19e940a03c user: richard_burhans date: 2012-03-22 21:15:24 summary: fix get_file_peek() to better support datasets with very long lines affected #: 1 file diff -r fa40b8f3f385f67d57294d98a036e483775d873f -r bb19e940a03c7120674b2ba1ebf1588cbea95f74 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -433,13 +433,13 @@ if line and not line.startswith( '#' ): data_lines += 1 return data_lines - def set_peek( self, dataset, line_count=None, is_multi_byte=False, skipchars=[] ): + def set_peek( self, dataset, line_count=None, is_multi_byte=False, WIDTH=256, skipchars=[] ): """ Set the peek. This method is used by various subclasses of Text. """ if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, skipchars=skipchars ) + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, WIDTH=WIDTH, skipchars=skipchars ) if line_count is None: # See if line_count is stored in the metadata if dataset.metadata.data_lines: @@ -567,6 +567,11 @@ ## >>> get_file_peek(fname) ## 'chr22 30128507 31828507 uc003bnx.1_cds_2_0_chr22_29227_f 0 +\n' """ + # Set size for file.readline() to a negative number to force it to + # read until either a newline or EOF. Needed for datasets with very + # long lines. + if WIDTH == 'unlimited': + WIDTH = -1 lines = [] count = 0 file_type = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: richard_burhans: changes to aaChanges tool
by Bitbucket 22 Mar '12

22 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/fa40b8f3f385/ changeset: fa40b8f3f385 user: richard_burhans date: 2012-03-22 18:19:31 summary: changes to aaChanges tool affected #: 2 files diff -r 1f6c7be22ba9059d8fd8e05148466bb005a7fbd1 -r fa40b8f3f385f67d57294d98a036e483775d873f tools/evolution/codingSnps.pl --- a/tools/evolution/codingSnps.pl +++ b/tools/evolution/codingSnps.pl @@ -7,11 +7,15 @@ # and a gene bed file with cds start and stop. # It then checks for changes in coding regions, reporting # those that cause a frameshift or substitution in the amino acid. +# Output columns: +# chrom, start, end, allele as given (amb code translated) +# Gene ID from genes file, ref amino acid:variant amino acids, +# codon number, (in strand of gene)ref nt, refCodon:variantCodons ######################################################################### my $seqFlag = "2bit"; #flag to set sequence type 2bit|nib if (!@ARGV or scalar @ARGV < 3) { - print "Usage: codingSnps.pl snps.bed genes.bed (/dir/*$seqFlag|Galaxy build= loc=) [chr=# start=# end=# snp=# keepColumns=1] > codingSnps.txt\n"; + print "Usage: codingSnps.pl snps.bed genes.bed (/dir/*$seqFlag|Galaxy build= loc=) [chr=# start=# end=# snp=# strand=#|-|+ keepColumns=1 synon=1 unique=1] > codingSnps.txt\n"; exit; } my $uniq = 0; #flag for whether want uniq positions @@ -25,6 +29,7 @@ my $col1 = 1; my $col2 = 2; my $col3 = 3; +my $strand = -1; #column positions 1 based coming in (for Galaxy) foreach (@ARGV) { if (/chr=(\d+)/) { $col0 = $1 -1; } @@ -32,6 +37,10 @@ elsif (/end=(\d+)/) { $col2 = $1 -1; } elsif (/snp=(\d+)/) { $col3 = $1 -1; } elsif (/keepColumns=1/) { $keep = 1; } + elsif (/synon=1/) { $syn = 1; } + elsif (/unique=1/) { $uniq = 1; } + elsif (/strand=(\d+)/) { $strand = $1 -1; } #0 based column + elsif (/strand=-/) { $strand = -99; } #special case of all minus } if ($col0 < 0 || $col1 < 0 || $col2 < 0 || $col3 < 0) { print STDERR "ERROR column numbers are given with origin 1\n"; @@ -42,6 +51,7 @@ my %codon; #hash of codon amino acid conversions my $ends = 0; #ends vs sizes in bed 11 position, starts relative to chrom my $ignoreN = 1; #skip N +my $origAll; #alleles from input file (before changes for strand) my %amb = ( "R" => "A/G", @@ -90,6 +100,10 @@ print STDERR "ERROR file has fewer columns than requested, requested columns (0 based) $col0 $col1 $col2 $col3, file has $size\n"; exit 1; } + if ($strand >= 0 && $strand > $size) { + print STDERR "ERROR file has fewer columns than requested, requested strand in $strand (0 based), file has $size\n"; + exit 1; + } if ($s[$col1] =~ /\D/) { print STDERR "ERROR the start point must be an integer not $s[$col1]\n"; exit 1; @@ -100,6 +114,11 @@ } if ($s[$col3] eq 'N' && $ignoreN) { next; } if (exists $amb{$s[$col3]}) { $s[$col3] = $amb{$s[$col3]}; } + if (($strand >= 0 && $s[$strand] eq '-') or $strand == -99) { + #reverse complement nts + $origAll = $s[$col3]; + $s[$col3] = reverseCompAlleles($s[$col3]); + }else { undef $origAll } if (!@g && exists $chrSt{$s[$col0]}) { #need to fetch first gene row $i = $chrSt{$s[$col0]}; @g = split(/\t/, $genes[$i]); @@ -287,36 +306,45 @@ } #now compute amino acids my $oldaa = getaa($oldnts); + my $codon = "$oldnts:"; my @newaa; my $change = 0; #flag for if there is a change foreach my $v (@newnts) { my $t = getaa($v); if ($t ne $oldaa) { $change = 1; } - push(@newaa, $t); + push(@newaa, "$t"); + $codon .= "$v/"; } + $codon =~ s/\/$//; if (!$change && $syn) { if (!$keep) { print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; }else { my @s = @{$sref}; print join("\t", @s), - "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\n"; + "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; } + $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; return; }elsif ($syn) { return; } #only want synonymous changes if (!$change) { return; } #no change in amino acids if (!$keep) { - print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$sref->[$col3]"; - if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + my $a = $sref->[$col3]; + if (($strand >= 0 && $origAll) or $strand == -99) { $a = $origAll; } + print "$sref->[$col0]\t$sref->[$col1]\t$sref->[$col2]\t$a"; + #my $minus = $changed; #in case minus strand and change back + #if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref if (!$changed) { return; } #skip this one - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; }else { my @s = @{$sref}; + if (($strand >= 0 && $origAll) or $strand == -99) { $s[$col3] = $origAll; } print join("\t", @s); - if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref + #my $minus = $changed; #in case minus strand and change back + #if ($gref->[5] eq '-') { $changed = compl($changed); } #use plus for ref if (!$changed) { return; } #skip this one - print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\n"; + print "\t$gref->[3]\t$oldaa:", join("/", @newaa), "\t$cdNum\t$changed\t$codon\n"; } $done{"$sref->[$col0] $sref->[$col1] $sref->[$col2]"}++; } @@ -418,6 +446,19 @@ return $comp; } +sub reverseCompAlleles { + my $all = shift; + my @nt = split(/\//, $all); + my $rv = ''; + foreach my $n (@nt) { + $n = reverse(split(/ */, $n)); #needed for indels + $n = compl($n); + $rv .= "$n/"; + } + $rv =~ s/\/$//; + return $rv; +} + sub getaa { my $nts = shift; #in multiples of 3 my $aa = ''; diff -r 1f6c7be22ba9059d8fd8e05148466bb005a7fbd1 -r fa40b8f3f385f67d57294d98a036e483775d873f tools/evolution/codingSnps.xml --- a/tools/evolution/codingSnps.xml +++ b/tools/evolution/codingSnps.xml @@ -2,7 +2,7 @@ <description>amino-acid changes caused by a set of SNPs</description><command interpreter="perl"> - codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep > $out_file1 + codingSnps.pl $input1 $input2 Galaxy build=${input1.metadata.dbkey} loc=${GALAXY_DATA_INDEX_DIR}/codingSnps.loc chr=${input1.metadata.chromCol} start=${input1.metadata.startCol} end=${input1.metadata.endCol} snp=$col1 keepColumns=$keep strand=${strand_source.strand_col} > $out_file1 </command><inputs> @@ -17,6 +17,22 @@ <option value="0" selected="true">No</option><option value="1">Yes</option></param> + <conditional name="strand_source"> + <param name="strand_choice" type="select" label="Strand info"> + <option value="data_column">a column in the dataset</option> + <option value="all_pos" selected="true">all on sense/forward/+ strand</option> + <option value="all_neg">all on antisense/reverse/- strand</option> + </param> + <when value="data_column"> + <param name="strand_col" type="data_column" data_ref="input1" label="Column with strand"/> + </when> + <when value="all_pos"> + <param name="strand_col" type="hidden" value="+"/> + </when> + <when value="all_neg"> + <param name="strand_col" type="hidden" value="-"/> + </when> + </conditional></inputs><outputs> @@ -36,14 +52,26 @@ <param name="input1" ftype="interval" value="codingSnps_input1.interval" dbkey="hg18" /><param name="col1" value="6" /><param name="input2" ftype="interval" value="codingSnps_inputGenes1.bed" dbkey="hg18" /> + <param name="strand_choice" value="all_pos" /> + <param name="strand_col" value="+" /><output name="output" file="codingSnps_output1.interval" /></test><test><param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" /><param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" /><param name="col1" value="4" /> + <param name="strand_choice" value="all_pos" /> + <param name="strand_col" value="+" /><output name="output" file="codingSnps_output2.interval" /></test> + <test> + <param name="input1" ftype="interval" value="codingSnps_input2.interval" dbkey="hg18" /> + <param name="input2" ftype="interval" value="codingSnps_inputGenes2.bed" dbkey="hg18" /> + <param name="col1" value="4" /> + <param name="strand_choice" value="all_neg" /> + <param name="strand_col" value="-" /> + <output name="output" file="codingSnps_output3.interval" /> + </test></tests><help> @@ -79,8 +107,9 @@ the first 12 columns standard BED columns. The output is the same as the first input file with several columns added: the name field from the line of the gene input file -used, the amino acids, the codon number, and the reference nucleotide that -changed in the amino acid. +used, the amino acids, the codon number, the reference nucleotide that +changed in the amino acid (in the same strand as the gene), and the codons +that go with the amino acids. The amino acids are listed with the reference amino acid first, then a colon, and then the amino acids for the alleles. If a SNP is not in a coding region or is synonymous then it is not included in the output file. @@ -128,15 +157,15 @@ - output file, showing non-synonymous substitutions in coding regions:: - chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 T - chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 C - chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 C - chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 C - chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 A - chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 T - chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 G - chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 G - chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 C + chr22 15825725 15825726 G/T uc002zlw.1 Gln:Pro/Gln 469 A CAA:CCA/CAA + chr22 15827035 15827036 G uc002zlw.1 Glu:Asp 414 G GAG:GAC + chr22 15827135 15827136 C/G uc002zlw.1 Gly:Gly/Ala 381 G GGT:GGT/GCT + chr22 15830928 15830929 A/G uc002zlw.1 Ala:Ser/Pro 281 G GCA:TCA/CCA + chr22 15830951 15830952 G uc002zlw.1 Leu:Pro 273 T CTT:CCT + chr22 15830955 15830956 C/T uc002zlw.1 Ser:Gly/Ser 272 A AGC:GGC/AGC + chr22 15848885 15848886 C/T uc002zlw.1 Ser:Trp/Stop 217 C TCG:TGG/TAG + chr22 15848885 15848886 C/T uc010gqs.1 Ser:Trp/Stop 200 C TCG:TGG/TAG + chr22 15849048 15849049 A/C uc002zlw.1 Gly:Stop/Gly 163 G GGA:TGA/GGA etc. </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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