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 <n...@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.pa...@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 <h...@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 <h...@fmi.ch
> >> <mailto:h...@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.pa...@cruk.cam.ac.uk <mailto:anne.pa...@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.pa...@cruk.cam.ac.uk <mailto:anne.pa...@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.pa...@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.pa...@cruk.cam.ac.uk | +44 (0)1223 769 631

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