Yes - it works there from a slightly faked Galaxy url so I think you've nailed it thanks. Please let me know when you've rolled this out to production? Thanks again for sorting this out so efficiently.
On Mon, Feb 9, 2009 at 9:05 PM, Ross Lazarus <[email protected]> wrote: > Goodness me - thank you! That was quick! Yes, I'll try to test it as > soon as I can. > > On Mon, Feb 9, 2009 at 8:43 PM, Jennifer Jackson <[email protected]> wrote: >> Hello Ross, >> >> We have isolated your problem and are in the process of implementing/testing >> the fix. Meanwhile, you are welcome to use/test along with us at >> http://genome-test.cse.ucsc.edu/ >> >> Please let us know if you have any problems or observations, >> Jennifer Jackson >> UCSC Genome Bioinformatics Group >> >> Ross Lazarus wrote: >>> >>> 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 MBBS MPH > Associate Professor, Department of Ambulatory Care and Prevention > Director of Bioinformatics, Channing Laboratory > 181 Longwood Ave., Boston MA 02115, USA. > Tel: +617 525 2730 Fax: +617 525 0958 > -- Ross Lazarus MBBS MPH Associate Professor, Department of Ambulatory Care and Prevention Director of Bioinformatics, Channing Laboratory 181 Longwood Ave., Boston MA 02115, USA. Tel: +617 525 2730 Fax: +617 525 0958 _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
