Re: [galaxy-dev] Galaxy CloudMan instance - missing link 'display at UCSC' for bed files
Many thanks for helping. Here is what I found in the universe_wsgi.ini ucsc_display_sites = main,test,archaea,ucla Where else should I look? Any other suggestions… many thanks in advance. Best regards, Anne. On 16 Feb 2015, at 12:30, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Anne
Have you also checked 'universe_wsgi.ini' to make sure it contains:
ucsc_display_sites = main
Though, this might me stored in config/galaxy.ini in the current Galaxy CloudMan code
Hans-Rudolf
On 02/16/2015 12:29 PM, Anne Pajon wrote:
Hi Hans,
Many thanks for your suggestion. I’ve looked at ucsc_build_sites.txt and its content is:
#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn mainhttp://genome.ucsc.edu/cgi-bin/hgTracks?priPac1,danRer4,mm9,mm8,droAna1,mm5,... #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaeahttp://archaea.ucsc.edu/cgi-bin/hgTracks?alkaEhrl_MLHE_1,shewW318,idioLoih_L... eot_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_T ULARENSIS,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_CGDN IH1,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 testhttp://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?anoCar1,ce4,ce3,ce2,ce1,lox... ,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 uclahttp://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?araTha1
It does contain hg19, the genome of the bed file I am trying to get displayed at UCSC but I still do not have the link to do so… any other ideas where I should look? Many thanks in advance.
Best regards, Anne.
On 16 Feb 2015, at 08:01, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Anne
Have you also checked: ~/tool-data/shared/ucsc/ucsc_build_sites.txt to make sure the the 'genome' of your bed file is actually listed ?
Regards, Hans-Rudolf
On 02/13/2015 07:05 PM, Anne Pajon wrote:
Dear All,
I’ve installed a Galaxy CloudMan instance on amazon for a training course we will be giving at the end of the month, as a re-run of a course we did last September. I am facing a problem as I am unable to get the link 'display at UCSC’ for our bed files, and it was not the case back in September.
So far, I’ve edited /mnt/galaxy/galaxy-app/datatypes_conf.xml in our cloud instance and uncommented <display file="ucsc/interval_as_bed.xml" /> but it did not change anything after a re-start. Any ideas what could have changed? Or how I could turn this back on? Any help would be greatly appreciated otherwise I will have to rewrite part of the training materials… Many thanks in advance.
Best wishes, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
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-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
On 02/16/2015 02:53 PM, Anne Pajon wrote:
Many thanks for helping. Here is what I found in the universe_wsgi.ini ucsc_display_sites = main,test,archaea,ucla Where else should I look? Any other suggestions… many thanks in advance.
I am sorry, I am running out of ideas. Maybe it is something "CloudMan" specific? Hans-Rudolf
Best regards, Anne.
On 16 Feb 2015, at 12:30, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Anne
Have you also checked 'universe_wsgi.ini' to make sure it contains:
ucsc_display_sites = main
Though, this might me stored in config/galaxy.ini in the current Galaxy CloudMan code
Hans-Rudolf
On 02/16/2015 12:29 PM, Anne Pajon wrote:
Hi Hans,
Many thanks for your suggestion. I’ve looked at ucsc_build_sites.txt and its content is:
#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn mainhttp://genome.ucsc.edu/cgi-bin/hgTracks?priPac1,danRer4,mm9,mm8,droAna1,mm5,... #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaeahttp://archaea.ucsc.edu/cgi-bin/hgTracks?alkaEhrl_MLHE_1,shewW318,idioLoih_L... nG eot_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,franTul a_T ULARENSIS,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_C GDN IH1,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 testhttp://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?anoCar1,ce4,ce3,ce2,ce1,lox... _1 ,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 uclahttp://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?araTha1
It does contain hg19, the genome of the bed file I am trying to get displayed at UCSC but I still do not have the link to do so… any other ideas where I should look? Many thanks in advance.
Best regards, Anne.
On 16 Feb 2015, at 08:01, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Anne
Have you also checked: ~/tool-data/shared/ucsc/ucsc_build_sites.txt to make sure the the 'genome' of your bed file is actually listed ?
Regards, Hans-Rudolf
On 02/13/2015 07:05 PM, Anne Pajon wrote:
Dear All,
I’ve installed a Galaxy CloudMan instance on amazon for a training course we will be giving at the end of the month, as a re-run of a course we did last September. I am facing a problem as I am unable to get the link 'display at UCSC’ for our bed files, and it was not the case back in September.
So far, I’ve edited /mnt/galaxy/galaxy-app/datatypes_conf.xml in our cloud instance and uncommented <display file="ucsc/interval_as_bed.xml" /> but it did not change anything after a re-start. Any ideas what could have changed? Or how I could turn this back on? Any help would be greatly appreciated otherwise I will have to rewrite part of the training materials… Many thanks in advance.
Best wishes, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
Hi Anne, The "display sites" options moved from the Galaxy config (universe_wsgi.ini or galaxy.ini) to datatypes_conf.xml. Have a look at the <build_sites> section in datatypes_conf.xml.sample, and it's not there in your datatypes_conf.xml, copy it over. --nate On Mon, Feb 16, 2015 at 8:53 AM, Anne Pajon <Anne.Pajon@cruk.cam.ac.uk> wrote:
Many thanks for helping. Here is what I found in the universe_wsgi.ini ucsc_display_sites = main,test,archaea,ucla Where else should I look? Any other suggestions… many thanks in advance. Best regards, Anne.
On 16 Feb 2015, at 12:30, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Anne
Have you also checked 'universe_wsgi.ini' to make sure it contains:
ucsc_display_sites = main
Though, this might me stored in config/galaxy.ini in the current Galaxy CloudMan code
Hans-Rudolf
On 02/16/2015 12:29 PM, Anne Pajon wrote:
Hi Hans,
Many thanks for your suggestion. I’ve looked at ucsc_build_sites.txt and its content is:
#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn mainhttp:// 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,hg19 #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaeahttp:// 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,deinG
eot_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_T
ULARENSIS,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_CGDN
IH1,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 testhttp:// genome-test.cse.ucsc.edu/cgi-bin/hgTracks?anoCar1,ce4,ce3,ce2,ce1,loxAfr1,rn2,eschColi_O157H7_1,rn4,droYak1,heliPylo_J99_1,droYak2,dp3,dp2,caeRem2,caeRem1,oryLat1,eschColi_K12_1,homIni13,homIni14,droAna1,droAna2,oryCun1,sacCer1,heliHepa1,droGri1,sc1,dasNov1,choHof1,tupBel1,mm9,mm8,vibrChol1,mm5,mm4,mm7,mm6,mm3,mm2,rn3,venter1,galGal3,galGal2,ornAna1,equCab1,cioSav2,rheMac2,eutHer13,droPer1,droVir2,droVir1,heliPylo_26695_1,euaGli13,calJac1,campJeju1,droSim1,hg13,hg15,hg16,hg17,monDom1,monDom4,droMoj1,petMar1,droMoj2,vibrChol_MO10_1,vibrPara1,gliRes13,vibrVuln_YJ016_1,braFlo1,cioSav1,lauRas13,dm1,canFam1,canFam2,ci1,echTel1,ci2,caePb1,dm3,ponAbe2,falciparum,xenTro1,xenTro2,nonAfr13,fr2,fr1,gasAcu1,dm2,apiMel1,apiMel2,eschColi_O157H7EDL933_1,priPac1,panTro1,hg18,panTro2,campJeju_RM1221_1,canHg12,vibrChol_O395_1,vibrFisc_ES114_1,danRer5,danRer4,danRer3,danRer2,danRer1,tetNig1,afrOth13,bosTau1,eschColi_CFT073_1,bosTau3,bosTau2,bosTau4,rodEnt13,droEre1,priMat13,vibrVuln_CMCP6_1
,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2
uclahttp://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?araTha1
It does contain hg19, the genome of the bed file I am trying to get displayed at UCSC but I still do not have the link to do so… any other ideas where I should look? Many thanks in advance.
Best regards, Anne.
On 16 Feb 2015, at 08:01, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Anne
Have you also checked: ~/tool-data/shared/ucsc/ucsc_build_sites.txt to make sure the the 'genome' of your bed file is actually listed ?
Regards, Hans-Rudolf
On 02/13/2015 07:05 PM, Anne Pajon wrote:
Dear All,
I’ve installed a Galaxy CloudMan instance on amazon for a training course we will be giving at the end of the month, as a re-run of a course we did last September. I am facing a problem as I am unable to get the link 'display at UCSC’ for our bed files, and it was not the case back in September.
So far, I’ve edited /mnt/galaxy/galaxy-app/datatypes_conf.xml in our cloud instance and uncommented <display file="ucsc/interval_as_bed.xml" /> but it did not change anything after a re-start. Any ideas what could have changed? Or how I could turn this back on? Any help would be greatly appreciated otherwise I will have to rewrite part of the training materials… Many thanks in advance.
Best wishes, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
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-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Hi Nate, Many thanks for telling me this. I did not know that the display sites options have moved. To summarise for others, I’ve only updated the /mnt/galaxy/galaxy-app/datatypes_conf.xml and added at the end the <build_sites></build_sites> section copied from /mnt/galaxy/galaxy-app/config/datatypes_conf.xml.sample. Maybe cloudman people would like to update their config. Do you know who I should contact? Many thanks again for your help. Kind regards, Anne. On 16 Feb 2015, at 16:39, Nate Coraor <nate@bx.psu.edu> wrote:
Hi Anne,
The "display sites" options moved from the Galaxy config (universe_wsgi.ini or galaxy.ini) to datatypes_conf.xml. Have a look at the <build_sites> section in datatypes_conf.xml.sample, and it's not there in your datatypes_conf.xml, copy it over.
--nate
On Mon, Feb 16, 2015 at 8:53 AM, Anne Pajon <Anne.Pajon@cruk.cam.ac.uk> wrote: Many thanks for helping. Here is what I found in the universe_wsgi.ini ucsc_display_sites = main,test,archaea,ucla Where else should I look? Any other suggestions… many thanks in advance. Best regards, Anne.
On 16 Feb 2015, at 12:30, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Anne
Have you also checked 'universe_wsgi.ini' to make sure it contains:
ucsc_display_sites = main
Though, this might me stored in config/galaxy.ini in the current Galaxy CloudMan code
Hans-Rudolf
On 02/16/2015 12:29 PM, Anne Pajon wrote:
Hi Hans,
Many thanks for your suggestion. I’ve looked at ucsc_build_sites.txt and its content is:
#Harvested from http://genome.ucsc.edu/cgi-bin/das/dsn mainhttp://genome.ucsc.edu/cgi-bin/hgTracks?priPac1,danRer4,mm9,mm8,droAna1,mm5,... #Harvested from http://archaea.ucsc.edu/cgi-bin/das/dsn archaeahttp://archaea.ucsc.edu/cgi-bin/hgTracks?alkaEhrl_MLHE_1,shewW318,idioLoih_L... eot_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_T ULARENSIS,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_CGDN IH1,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 testhttp://genome-test.cse.ucsc.edu/cgi-bin/hgTracks?anoCar1,ce4,ce3,ce2,ce1,lox... ,cb2,cb3,cb1,borEut13,droSec1,felCat3,strPur1,strPur2,otoGar1,catArr1,anoGam1,triCas2 uclahttp://epigenomics.mcdb.ucla.edu/cgi-bin/hgTracks?araTha1
It does contain hg19, the genome of the bed file I am trying to get displayed at UCSC but I still do not have the link to do so… any other ideas where I should look? Many thanks in advance.
Best regards, Anne.
On 16 Feb 2015, at 08:01, Hans-Rudolf Hotz <hrh@fmi.ch <mailto:hrh@fmi.ch>> wrote:
Hi Anne
Have you also checked: ~/tool-data/shared/ucsc/ucsc_build_sites.txt to make sure the the 'genome' of your bed file is actually listed ?
Regards, Hans-Rudolf
On 02/13/2015 07:05 PM, Anne Pajon wrote:
Dear All,
I’ve installed a Galaxy CloudMan instance on amazon for a training course we will be giving at the end of the month, as a re-run of a course we did last September. I am facing a problem as I am unable to get the link 'display at UCSC’ for our bed files, and it was not the case back in September.
So far, I’ve edited /mnt/galaxy/galaxy-app/datatypes_conf.xml in our cloud instance and uncommented <display file="ucsc/interval_as_bed.xml" /> but it did not change anything after a re-start. Any ideas what could have changed? Or how I could turn this back on? Any help would be greatly appreciated otherwise I will have to rewrite part of the training materials… Many thanks in advance.
Best wishes, Anne. -- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk <mailto:anne.pajon@cruk.cam.ac.uk> | +44 (0)1223 769 631
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Dr Anne Pajon - Bioinformatics Core Cancer Research UK - Cambridge Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cruk.cam.ac.uk | +44 (0)1223 769 631
participants (3)
-
Anne Pajon -
Hans-Rudolf Hotz -
Nate Coraor