Hi Arek, Thank you very much for your reply and help. It seems that when running ./dist/scripts/martconfigurator.sh in my terminal the GUI works. When importing from ensembl all the organisms using "ADD SOURCE" it also works. When trying to configure the "root" of hsapiens_gene_ensembl_config - there are yellow triangles on the Attributes and Filters. Also after saving .xml file and opening a server trying to configure the attributes and filters via web doesn't give any results.
Thanks, Tom. On Sun, Aug 5, 2012 at 7:39 PM, Arek Kasprzyk <[email protected]>wrote: > Hi Tom, > can you confirm that the portal is running ok on your laptop, ei you can > click on the GUI and get your queries working interactively? > > is it just the programmatic access that is the problem? > > a > > On Sun, Aug 5, 2012 at 10:38 AM, Tom Hait <[email protected]> wrote: > >> Hello, >> >> My name is Tom and i'm a student in bioinformatics. >> I installed biomart version 0.8 as instructed in page 5 of the manual. >> than I tried to run some examples: >> exapmle 1 from page 75 - query.xml >> I got the result: >> *<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" " >> http://www.w3.org/TR/html4/loose.dtd";>* *<HTML><HEAD><META >> HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">* >> *<TITLE>ERROR: >> The requested URL could not be retrieved</TITLE>* *<STYLE >> type="text/css"><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE> >> * *</HEAD><BODY>* *<H1>ERROR</H1>* *<H2>The requested URL could not be >> retrieved</H2>* *<HR noshade size="1px">* *<P>* *While trying to >> retrieve the URL:* *<A HREF="http://localhost:9000/martservice/results";> >> http://localhost:9000/martservice/results</A>* *<P>* *The following >> error was encountered:* *<UL>* *<LI>* *<STRONG>* *Connection to >> 127.0.0.1 Failed* *</STRONG>* *</UL>* >> it couldn't connect to biomart server. >> than i tried to run the example from page 92 and the results are that it >> couldn't find the relevant packages - portal.java, query.java etc. >> >> I will appreciate any kind of help, >> >> Best regards, >> >> Tom. >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > www.biomart.org >
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
