diff --git a/lib/galaxy/security/__init__.py b/lib/galaxy/security/__init__.py index 730b2147f31..fa0a6650bdc 100644 --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -1005,8 +1005,7 @@ class HostAgent( RBACAgent ): ucsc_main = ( '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' ), ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ), - ucsc_bhri = ('ucsc.omics.bhri.internal','galaxy.omics.bhri.internal'), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) ) def __init__( self, model, permitted_actions=None ): self.model = model @@ -1037,7 +1036,7 @@ class HostAgent( RBACAgent ): # We're going to search in order, but if the remote site is load # balancing their connections (as UCSC does), this is okay. try: - if socket.gethostbyname( server ) == addr or server == '127.0.0.1' or server == '172.16.0.38': + if socket.gethostbyname( server ) == addr: break # remote host is in the server list except ( socket.error, socket.gaierror ): pass # can't resolve, try next diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index ebbdbed9fcf..c45019061a1 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -922,8 +922,6 @@ class Tool: if not self.check_values: return for input in self.inputs.itervalues(): - if input.name not in value: - value[input.name] = input.get_initial_value( None, value ) if isinstance( input, ToolParameter ): callback( "", input, value[input.name] ) else: diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 7927d9b9e65..4fef3efafe0 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -748,6 +748,9 @@ class SelectToolParameter( ToolParameter ): # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ): return True + #dataset not ready yet + if hasattr( self, 'ref_input' ) and isinstance( dep_value, self.tool.app.model.HistoryDatasetAssociation ) and ( dep_value.is_pending or not isinstance( dep_value.datatype, self.ref_input.formats ) ): + return True # Dynamic, but all dependenceis are known and have values return False def get_initial_value( self, trans, context ): @@ -878,6 +881,7 @@ class ColumnListParameter( SelectToolParameter ): self.force_select = string_as_bool( elem.get( "force_select", True )) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) + self.ref_input = None self.default_value = elem.get( "default_value", None ) self.is_dynamic = True def from_html( self, value, trans=None, context={} ): @@ -973,7 +977,7 @@ class ColumnListParameter( SelectToolParameter ): if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready # (since we have reason to expect the metadata to be ready eventually) - if dataset.is_pending: + if dataset.is_pending or not isinstance( dataset.datatype, self.ref_input.formats ): return True # No late validation return False @@ -1353,7 +1357,7 @@ class DataToolParameter( ToolParameter ): selected = ( value and ( hda in value ) ) field.add_option( "%s: %s" % ( hid, hda_name ), hda.id, selected ) else: - target_ext, converted_dataset = hda.find_conversion_destination( self.formats, converter_safe = self.converter_safe( other_values, trans ) ) + target_ext, converted_dataset = hda.find_conversion_destination( self.formats ) if target_ext: if converted_dataset: hda = converted_dataset @@ -1402,13 +1406,22 @@ class DataToolParameter( ToolParameter ): pass #no valid options def dataset_collector( datasets ): def is_convertable( dataset ): - target_ext, converted_dataset = dataset.find_conversion_destination( self.formats, converter_safe = self.converter_safe( context, trans ) ) + target_ext, converted_dataset = dataset.find_conversion_destination( self.formats ) if target_ext is not None: return True return False for i, data in enumerate( datasets ): - if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED] and ( isinstance( data.datatype, self.formats) or is_convertable( data ) ): - if self.options and self._options_filter_attribute( data ) != filter_value: + if data.visible and not data.deleted and data.state not in [data.states.ERROR, data.states.DISCARDED]: + is_valid = False + if isinstance( data.datatype, self.formats ): + is_valid = True + else: + target_ext, converted_dataset = data.find_conversion_destination( self.formats ) + if target_ext: + is_valid = True + if converted_dataset: + data = converted_dataset + if not is_valid or ( self.options and self._options_filter_attribute( data ) != filter_value ): continue most_recent_dataset[0] = data # Also collect children via association object diff --git a/lib/galaxy/web/framework/middleware/remoteuser.py b/lib/galaxy/web/framework/middleware/remoteuser.py index 89fad1c0e67..ec56acb8119 100644 --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -36,7 +36,6 @@ errorpage = """ """ UCSC_MAIN_SERVERS = ( - 'omics.bhri.internal', 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', @@ -50,7 +49,6 @@ UCSC_ARCHAEA_SERVERS = ( 'lowepub.cse.ucsc.edu', ) - class RemoteUser( object ): def __init__( self, app, maildomain=None, ucsc_display_sites=[], admin_users=[] ): self.app = app @@ -58,7 +56,7 @@ class RemoteUser( object ): self.allow_ucsc_main = False self.allow_ucsc_archaea = False self.admin_users = admin_users - if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites or 'bhri' in ucsc_display_sites: + if 'main' in ucsc_display_sites or 'test' in ucsc_display_sites: self.allow_ucsc_main = True if 'archaea' in ucsc_display_sites: self.allow_ucsc_archaea = True diff --git a/scripts/cleanup_datasets/purge_libraries.sh b/scripts/cleanup_datasets/purge_libraries.sh index 9166c341c99..d95c8b5cd4d 100644 --- a/scripts/cleanup_datasets/purge_libraries.sh +++ b/scripts/cleanup_datasets/purge_libraries.sh @@ -1,5 +1,4 @@ #!/bin/sh cd `dirname $0`/../.. -#python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 2 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log +python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log diff --git a/templates/admin/dataset_security/group/grid.mako b/templates/admin/dataset_security/group/grid.mako old mode 100755 new mode 100644 diff --git a/templates/admin/dataset_security/group/group.mako b/templates/admin/dataset_security/group/group.mako old mode 100755 new mode 100644 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a/templates/tracks/history_select_grid.mako b/templates/tracks/history_select_grid.mako old mode 100755 new mode 100644 diff --git a/templates/tracks/index.mako b/templates/tracks/index.mako old mode 100755 new mode 100644 diff --git a/templates/tracks/new_browser.mako b/templates/tracks/new_browser.mako old mode 100755 new mode 100644 diff --git a/templates/user/dbkeys.mako b/templates/user/dbkeys.mako old mode 100755 new mode 100644 diff --git a/templates/user/edit_address.mako b/templates/user/edit_address.mako old mode 100755 new mode 100644 diff --git a/templates/user/index.mako b/templates/user/index.mako old mode 100755 new mode 100644 diff --git a/templates/user/info.mako b/templates/user/info.mako old mode 100755 new mode 100644 diff --git a/templates/user/login.mako b/templates/user/login.mako old mode 100755 new mode 100644 diff --git a/templates/user/logout.mako b/templates/user/logout.mako old mode 100755 new mode 100644 diff --git a/templates/user/new_address.mako b/templates/user/new_address.mako old mode 100755 new mode 100644 diff --git a/templates/user/openid_associate.mako b/templates/user/openid_associate.mako old mode 100755 new mode 100644 diff --git a/templates/user/openid_manage.mako b/templates/user/openid_manage.mako old mode 100755 new mode 100644 diff --git a/templates/user/permissions.mako b/templates/user/permissions.mako old mode 100755 new mode 100644 diff --git a/templates/user/register.mako b/templates/user/register.mako old mode 100755 new mode 100644 diff --git a/templates/user/reset_password.mako b/templates/user/reset_password.mako old mode 100755 new mode 100644 diff --git a/templates/visualization/create.mako b/templates/visualization/create.mako old mode 100755 new mode 100644 diff --git a/templates/visualization/display.mako b/templates/visualization/display.mako old mode 100755 new mode 100644 diff --git a/templates/visualization/embed.mako b/templates/visualization/embed.mako old mode 100755 new mode 100644 diff --git a/templates/visualization/item_content.mako b/templates/visualization/item_content.mako old mode 100755 new mode 100644 diff --git a/templates/visualization/list.mako b/templates/visualization/list.mako old mode 100755 new mode 100644 diff --git a/templates/visualization/list_published.mako b/templates/visualization/list_published.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/admin/center.mako b/templates/webapps/community/admin/center.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/admin/index.mako b/templates/webapps/community/admin/index.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/base_panels.mako b/templates/webapps/community/base_panels.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/category/create_category.mako b/templates/webapps/community/category/create_category.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/category/edit_category.mako b/templates/webapps/community/category/edit_category.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/category/grid.mako b/templates/webapps/community/category/grid.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/common/common.mako b/templates/webapps/community/common/common.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/index.mako b/templates/webapps/community/index.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/message.mako b/templates/webapps/community/message.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/community/user/info.mako b/templates/webapps/community/user/info.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/demo_sequencer/empty.mako b/templates/webapps/demo_sequencer/empty.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/demo_sequencer/index.mako b/templates/webapps/demo_sequencer/index.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/demo_sequencer/login.mako b/templates/webapps/demo_sequencer/login.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/demo_sequencer/redirect.mako b/templates/webapps/demo_sequencer/redirect.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/galaxy/admin/center.mako b/templates/webapps/galaxy/admin/center.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/galaxy/admin/index.mako b/templates/webapps/galaxy/admin/index.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/galaxy/user/api_keys.mako b/templates/webapps/galaxy/user/api_keys.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/galaxy/user/info.mako b/templates/webapps/galaxy/user/info.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/base_panels.mako b/templates/webapps/reports/base_panels.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/dataset_info.mako b/templates/webapps/reports/dataset_info.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/grid.mako b/templates/webapps/reports/grid.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/index.mako b/templates/webapps/reports/index.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/job_info.mako b/templates/webapps/reports/job_info.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_per_domain.mako b/templates/webapps/reports/jobs_per_domain.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_per_month_all.mako b/templates/webapps/reports/jobs_per_month_all.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_per_month_in_error.mako b/templates/webapps/reports/jobs_per_month_in_error.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_per_tool.mako b/templates/webapps/reports/jobs_per_tool.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_per_user.mako b/templates/webapps/reports/jobs_per_user.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_specified_month_all.mako b/templates/webapps/reports/jobs_specified_month_all.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_specified_month_in_error.mako b/templates/webapps/reports/jobs_specified_month_in_error.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_tool_per_month.mako b/templates/webapps/reports/jobs_tool_per_month.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/jobs_user_per_month.mako b/templates/webapps/reports/jobs_user_per_month.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/registered_users.mako b/templates/webapps/reports/registered_users.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/registered_users_per_month.mako b/templates/webapps/reports/registered_users_per_month.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/registered_users_specified_date.mako b/templates/webapps/reports/registered_users_specified_date.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/registered_users_specified_month.mako b/templates/webapps/reports/registered_users_specified_month.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/system.mako b/templates/webapps/reports/system.mako old mode 100755 new mode 100644 diff --git a/templates/webapps/reports/users_last_access_date.mako b/templates/webapps/reports/users_last_access_date.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/build_from_current_history.mako b/templates/workflow/build_from_current_history.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/configure_menu.mako b/templates/workflow/configure_menu.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/display.mako b/templates/workflow/display.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/edit_attributes.mako b/templates/workflow/edit_attributes.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/editor.mako b/templates/workflow/editor.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/editor_generic_form.mako b/templates/workflow/editor_generic_form.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/editor_tool_form.mako b/templates/workflow/editor_tool_form.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/embed.mako b/templates/workflow/embed.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/export.mako b/templates/workflow/export.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/index.mako b/templates/workflow/index.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/item_content.mako b/templates/workflow/item_content.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/list.mako b/templates/workflow/list.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/list_for_run.mako b/templates/workflow/list_for_run.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/list_published.mako b/templates/workflow/list_published.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/myexp_export.mako b/templates/workflow/myexp_export.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/myexp_export_content.mako b/templates/workflow/myexp_export_content.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/rename.mako b/templates/workflow/rename.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/run_complete.mako b/templates/workflow/run_complete.mako old mode 100755 new mode 100644 diff --git a/templates/workflow/sharing.mako b/templates/workflow/sharing.mako old mode 100755 new mode 100644 diff --git a/tool-data/shared/ucsc/ucsc_build_sites.txt b/tool-data/shared/ucsc/ucsc_build_sites.txt index 1554e1a6c4e..7e4207fa286 100644 --- a/tool-data/shared/ucsc/ucsc_build_sites.txt +++ b/tool-data/shared/ucsc/ucsc_build_sites.txt @@ -1,6 +1,5 @@ #Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn main http://genome.ucsc.edu/cgi-bin/hgTracks? priPac1,danRer4,mm9,mm8,droAna1,mm5,caeRem2,mm7,mm6,panTro1,dm3,panTro2,anoCar1,ce4,galGal3,galGal2,ce1,rn3,rn2,droMoj1,droMoj2,rn4,droYak1,droYak2,dp3,dp2,dm1,canFam1,danRer5,canFam2,danRer3,danRer2,ornAna1,ci2,ci1,tetNig1,bosTau1,bosTau3,bosTau2,equCab1,oryLat1,droAna2,droEre1,ponAbe2,rheMac2,sacCer1,droPer1,droSim1,monDom1,cb1,dm2,droSec1,strPur1,droVir2,droVir1,strPur2,sc1,xenTro1,droGri1,xenTro2,cb3,gasAcu1,caePb1,anoGam1,fr2,fr1,hg15,hg16,hg17,hg18,felCat3,apiMel2,monDom4,apiMel1,ce2 -bhri http://ucsc.omics.bhri.internal/cgi-bin/hgTracks? hg18,hg19,mm8,mm9,rn4 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaea http://archaea.ucsc.edu/cgi-bin/hgTracks? alkaEhrl_MLHE_1,shewW318,idioLoih_L2TR,sulSol1,erwiCaro_ATROSEPTICA,symbTher_IAM14863,moorTher_ATCC39073,therFusc_YX,methHung1,bradJapo,therElon,shewPutrCN32,pediPent_ATCC25745,mariMari_MCS10,nanEqu1,baciSubt,chlaTrac,magnMagn_AMB_1,chroViol,ralsSola,acidCryp_JF_5,erytLito_HTCC2594,desuVulg_HILDENBOROUG,pyrAer1,sulfToko1,shewANA3,paraSp_UWE25,geobKaus_HTA426,rhizEtli_CFN_42,uncuMeth_RCI,candBloc_FLORIDANUS,deinRadi,yersPest_CO92,saccEryt_NRRL_2338,rhodRHA1,candCars_RUDDII,burkMall_ATCC23344,eschColi_O157H7,burk383,psycIngr_37,rhodSpha_2_4_1,wolbEndo_OF_DROSOPHIL,burkViet_G4,propAcne_KPA171202,enteFaec_V583,campJeju_81_176,acidJS42,heliPylo_26695,pseuHalo_TAC125,chroSale_DSM3043,methVann1,archFulg1,neisMeni_Z2491_1,fusoNucl,vermEise_EF01_2,anabVari_ATCC29413,tropWhip_TW08_27,heliHepa,acinSp_ADP1,anapMarg_ST_MARIES,natrPhar1,haheChej_KCTC_2396,therPetr_RKU_1,neisGono_FA1090_1,colwPsyc_34H,desuPsyc_LSV54,hyphNept_ATCC15444,vibrChol1,deinGeot_DSM11300,strePyog_M1_GAS,franCcI3,salmTyph,metaSedu,lactSali_UCC118,trepPall,neisMeni_MC58_1,syntWolf_GOETTINGEN,flavJohn_UW101,methBoon1,haemSomn_129PT,shewLoihPV4,igniHosp1,haemInfl_KW20,haloHalo_SL1,ferrAcid1,sphiAlas_RB2256,candPela_UBIQUE_HTCC1,caldSacc_DSM8903,aerPer1,lactPlan,carbHydr_Z_2901,therTher_HB8,vibrVuln_YJ016_1,rhodPalu_CGA009,acidCell_11B,siliPome_DSS_3,therVolc1,haloWals1,rubrXyla_DSM9941,shewAmaz,nocaJS61,vibrVuln_CMCP6_1,sinoMeli,ureaUrea,baciHalo,bartHens_HOUSTON_1,nitrWino_NB_255,hypeButy1,methBurt2,polaJS66,mesoLoti,methMari_C7,caulCres,neisMeni_FAM18_1,acidBact_ELLIN345,caldMaqu1,salmEnte_PARATYPI_ATC,glucOxyd_621H,cytoHutc_ATCC33406,nitrEuro,therMari,coxiBurn,woliSucc,heliPylo_HPAG1,mesoFlor_L1,pyrHor1,methAeol1,procMari_CCMP1375,pyroArse1,oenoOeni_PSU_1,alcaBork_SK2,wiggBrev,actiPleu_L20,lactLact,methJann1,paraDeni_PD1222,borrBurg,pyroIsla1,orieTsut_BORYONG,shewMR4,methKand1,methCaps_BATH,onioYell_PHYTOPLASMA,bordBron,cenaSymb1,burkCeno_HI2424,franTula_TULARENSIS,pyrFur2,mariAqua_VT8,heliPylo_J99,psycArct_273_4,vibrChol_MO10_1,vibrPara1,rickBell_RML369_C,metAce1,buchSp,ehrlRumi_WELGEVONDEN,methLabrZ_1,chlaPneu_CWL029,thioCrun_XCL_2,pyroCali1,chloTepi_TLS,stapAure_MU50,novoArom_DSM12444,magnMC1,zymoMobi_ZM4,salmTyph_TY2,chloChlo_CAD3,azoaSp_EBN1,therTher_HB27,bifiLong,picrTorr1,listInno,bdelBact,gramFors_KT0803,sulfAcid1,geobTher_NG80_2,peloCarb,ralsEutr_JMP134,mannSucc_MBEL55E,syneSp_WH8102,methTherPT1,clavMich_NCPPB_382,therAcid1,syntAcid_SB,porpGing_W83,therNeut0,leifXyli_XYLI_CTCB0,shewFrig,photProf_SS9,thioDeni_ATCC25259,methMaze1,desuRedu_MI_1,burkThai_E264,campFetu_82_40,blocFlor,jannCCS1,nitrMult_ATCC25196,streCoel,soliUsit_ELLIN6076,pastMult,saliRube_DSM13855,methTher1,nostSp,shigFlex_2A,saccDegr_2_40,oceaIhey,dehaEthe_195,rhodRubr_ATCC11170,arthFB24,shewMR7,pireSp,anaeDeha_2CP_C,haloVolc1,dichNodo_VCS1703A,tricEryt_IMS101,mycoGeni,thioDeni_ATCC33889,methSmit1,geobUran_RF4,shewDeni,halMar1,desuHafn_Y51,methStad1,granBeth_CGDNIH1,therPend1,legiPneu_PHILADELPHIA,vibrChol_O395_1,nitrOcea_ATCC19707,campJeju_RM1221,methPetr_PM1,heliAcin_SHEEBA,eschColi_APEC_O1,peloTher_SI,haloHalo1,syntFuma_MPOB,xyleFast,gloeViol,leucMese_ATCC8293,bactThet_VPI_5482,xantCamp,sodaGlos_MORSITANS,geobSulf,roseDeni_OCH_114,coryEffi_YS_314,brucMeli,mycoTube_H37RV,vibrFisc_ES114_1,pyrAby1,burkXeno_LB400,polyQLWP,stapMari1,peloLute_DSM273,burkCeno_AU_1054,shewBalt,nocaFarc_IFM10152,ente638,mculMari1,saliTrop_CNB_440,neorSenn_MIYAYAMA,aquiAeol,dechArom_RCB,myxoXant_DK_1622,burkPseu_1106A,burkCepa_AMMD,methMari_C5_1,azorCaul2,methFlag_KT,leptInte,eschColi_K12,synePCC6,baumCica_HOMALODISCA,methBark1,pseuAeru,geobMeta_GS15,eschColi_CFT073,photLumi,metMar1,hermArse,campJeju,therKoda1,aeroHydr_ATCC7966,baciAnth_AMES,shewOnei,therTeng,lawsIntr_PHE_MN1_00 #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample index 86d691352f4..f0352e4b419 100644 --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -368,7 +368,6 @@
-