Hi! I am a newbie to using the UCSC genome site. I am trying to incorporate the functionality of Jim Kent's software (specifically his sequenceForBed program) into a Java package for designing primers for bisulfite-treated sequences. Since the program will only occasionally need to download sequences from the UCSC site, I am not going to host my own mirror of the UCSC site, but will just do remote mySql accesses to ucsc. I downloaded and built the sequenceForBed program on Cygwin, but when I tried to run it, I get the same message as indicated on the subject line. The relevant portions of my .hg.conf file are given below. Would greatly appreciate any help in getting past this problem B.Kumar
========================== .hg.conf (with comments removed) ==================== db.host=genome-mysql.cse.ucsc.edu db.user=genomep db.password=password db.port=3306 db.socket=/var/lib/mysql/mysql.sock defaultGenome=Human db.trackDb=trackDb db.grp=grp wiki.host=genomewiki.ucsc.edu wiki.userNameCookie=wikidb_mw1_UserName wiki.loggedInCookie=wikidb_mw1_UserID customTracks.host=<your specific host name> customTracks.user=<your specific MySQL user for this function> customTracks.password=<MySQL password for specified user> customTracks.useAll=yes customTracks.tmpdir=/data/tmp/ct browser.indelOptions=on central.db=hgcentral central.host=genome-mysql.cse.ucsc.edu central.user=genomep central.password=password central.domain=mylab.university.edu central.port=3306 central.socket=/var/lib/mysql/mysql.sock browser.background=../images/floret.jpg browser.documentRoot=/usr/local/apache/htdocs grepIndex.genbank=/data/tmp/grepIndex grepIndex.default=/gbdb hgTracks.trackReordering=on backupcentral.db=hgcentral backupcentral.host=genome-mysql.cse.ucsc.edu backupcentral.user=genomep backupcentral.password=password archivecentral.db=hgcentral archivecentral.host=genome-mysql.cse.ucsc.edu archivecentral.user=genomep archivecentral.password=password hgc.psxyPath=/hive/data/outside/GMT4.3.1/bin/psxy hgc.ps2rasterPath=/hive/data/outside/GMT4.3.1/bin/ps2raster hgc.ghostscriptPath=/usr/bin/ghostscript _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
