adding another UCSC mirror to display
Hi again, this may be a FAQ, sorry for that... How can I add an alternate UCSC mirror site (our local mirror) to galaxy so that everything that could be displayed at UCSC-main will have the UCSC-localmirror option? Besides... how can I remove the bx main mirror? I've tried to add a ${GALAXYROOT}/tool-data/shared/campus/campus_build_sites.txt but that's not enough... I've modified the ucsc/bam.xml file adding another dynamic_link section but that's not enough... any hint? Thanks again d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it */
Hi Davide, I was doing something similar. But I think my galaxy is a little older because the directories are not the same as yours. But anyway, here is what I did. I added a line to the ${GALAXYROOT}/data/galaxy/galaxy-dist/tool-data/shared/ucsc/ucsc_build_sites.txt file: local_main http://ucsc.gis.a-star.edu.sg/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 Then in universe_wsgi.ini, I modified this line by adding the name of the local mirror. universe_wsgi.ini: ucsc_display_sites = gis_main,main,test,archaea,ucla After restarting galaxy, it the local mirror will just show up together with the regular main and test. Hope this helps. Best regards, Chee Seng, Chan From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Davide Cittaro Sent: Thursday, May 20, 2010 9:43 PM To: galaxy-dev@bx.psu.edu Subject: [galaxy-dev] adding another UCSC mirror to display Hi again, this may be a FAQ, sorry for that... How can I add an alternate UCSC mirror site (our local mirror) to galaxy so that everything that could be displayed at UCSC-main will have the UCSC-localmirror option? Besides... how can I remove the bx main mirror? I've tried to add a ${GALAXYROOT}/tool-data/shared/campus/campus_build_sites.txt but that's not enough... I've modified the ucsc/bam.xml file adding another dynamic_link section but that's not enough... any hint? Thanks again d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro@ifom-ieo-campus.it<mailto:davide.cittaro@ifom-ieo-campus.it> */
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CHAN Chee Seng -
Davide Cittaro