Help please! I've been using GG from Galaxy for about 2 years but today, when I went to make some nice pictures for my grant renewal (!), there appears to be a new problem.
Using a Galaxy constructed url like this: http://genome.ucsc.edu/cgi-bin/hgGenome?db=hg18&hgGenome_dataSetName=Plink%20sample%20wga%20data%20case%20control%20_CaCo_gg.track&hgGenome_dataSetDescription=GalaxyGG_data&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess&hgGenome_columnLabels=first%20row&hgGenome_maxVal=&hgGenome_labelVals=&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D477%26display_app%3Ducsc&hgGenome_doSubmitUpload=submit the data appear to upload fine, but the page that tells me how many snp and where they mapped does not show the usual button to proceed to view the karyotype, and when I view the page source, it is clearly truncated in the middle of the form that usually shows that button - here's the source for the UCSC page I'm getting after uploading (apparently successfully!) - note where it ends - and no closing body or html tags: ====================source========================================================= <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN"> <HTML> <HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html;CHARSET=iso-8859-1"> <META http-equiv="Content-Script-Type" content="text/javascript"> <META HTTP-EQUIV="Pragma" CONTENT="no-cache"> <META HTTP-EQUIV="Expires" CONTENT="-1"> <TITLE> Data Upload Complete (62 bytes) </TITLE> <LINK REL="STYLESHEET" HREF="../style/HGStyle.css" TYPE="text/css"> </HEAD> <BODY BGCOLOR="#FFF9D2" LINK="#0000CC" VLINK="#330066" ALINK="#6600FF"><A NAME="TOP"></A> <TABLE BORDER=0 CELLPADDING=0 CELLSPACING=0 WIDTH="100%"> <!-- +++++++++++++++++++++ HOTLINKS BAR +++++++++++++++++++ --> <TR><TD COLSPAN=3 HEIGHT=40 > <table bgcolor="#000000" cellpadding="1" cellspacing="1" width="100%%" height="27"> <tr bgcolor="#2636D1"><td valign="middle"> <table BORDER=0 CELLSPACING=0 CELLPADDING=0 bgcolor="#2636D1" height="24"><TR> <TD VALIGN="middle"><font color="#89A1DE"> <A HREF="../index.html?org=Human&db=hg18&hgsid=1605988" class="topbar"> Home</A> <A HREF="../cgi-bin/hgGateway?org=Human&db=hg18&hgsid=1605988" class="topbar"> Genomes</A> <A HREF="../cgi-bin/hgBlat?command=start&org=Human&db=hg18&hgsid=1605988" class="topbar"> Blat</A> <A HREF="../cgi-bin/hgTables?org=Human&db=hg18&hgsid=1605988&hgta_doMainPage=1" class="topbar"> Tables</A> <A HREF="../cgi-bin/hgNear?org=Human&db=hg18&hgsid=1605988" class="topbar"> Gene Sorter</A> <A HREF="../cgi-bin/hgPcr?org=Human&db=hg18&hgsid=1605988" class="topbar"> PCR</A> <A HREF="../cgi-bin/hgGenome?org=Human&db=hg18&hgsid=1605988&hgGenome_doPsOutput=on" class="topbar"> PDF/PS</A> <A HREF="../cgi-bin/hgSession?org=Human&db=hg18&hgsid=1605988&hgS_doMainPage=1" class="topbar">Session</A> <A HREF="../FAQ/" class="topbar"> FAQ</A> <A HREF="../goldenPath/help/hgGenomeHelp.html" class="topbar"> Help</A> </font></TD> </TR></TABLE> </TD></TR></TABLE> </TD></TR> <!-- +++++++++++++++++++++ CONTENT TABLES +++++++++++++++++++ --> <TR><TD COLSPAN=3> <!--outer table is for border purposes--> <TABLE WIDTH="100%" BGCOLOR="#888888" BORDER="0" CELLSPACING="0" CELLPADDING="1"><TR><TD> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" BORDER="0" CELLSPACING="0" CELLPADDING="0"><TR><TD> <TABLE BGCOLOR="#D9E4F8" BACKGROUND="../images/hr.gif" WIDTH="100%"><TR><TD> <FONT SIZE="4"><b> Data Upload Complete (62 bytes)</b></FONT></TD></TR></TABLE> <TABLE BGCOLOR="#FFFEE8" WIDTH="100%" CELLPADDING=0><TR><TH HEIGHT=10></TH></TR> <TR><TD WIDTH=10> </TD><TD> <FORM ACTION="../cgi-bin/hgGenome"><INPUT TYPE=HIDDEN NAME="hgsid" VALUE="1605988">Loaded 15625346 elements from snp129 table for mapping.<BR> Mapped 226064 of 228694 (98.8%) of markers<BR> ====================source ends here =================================== -- Ross Lazarus, Associate Professor, DACP, Harvard Medical School. Director of Bioinformatics, Channing Laboratory, BWH 181 Longwood Ave., Boston MA 02115, USA. _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
