Hi Yue #1. The icgc3 config is not part of the central registry yet that is available over webservice from biomart.org<http://biomart.org>. For now you need to load it directly from a file called icgc3.XML available in the registry directory in biomart-java. Jonathan will be adding a dedicated section on the icgc deployment in the next rc5 release docs so hopefully this should be clear then
#2 I did not experience any issues with msd when testing recently. Perhaps someone else could comment on that? a On 2011-02-23, at 23:59, "Yue W Webster" <[email protected]<mailto:[email protected]>> wrote: Hello Arek, I am trying to install biomart on a server outside of Lilly firewall and seems to get a bit future in the process. However, I am still having difficulties and have to bother you again. Issue #1: After opening “Add Data Source” window. I couldn’t see icgc3.xml after I scrolled through n the [Marts] list. <ATT00003..gif> Issue #2: Not able to find icgi, I tried to add MSD as mentioned in the installation document (BioMart 0.8 User Manual, release candidate 4, 1st February 2010). But after I clicked on msd proteinstructures and clicked OK, I was never prompted to choose a name. Nor was a new config created and shown in the right-hand panel. Here is the message from the terminal Starting MartConfigurator please wait .... [Thread-3] ERROR martconfigurator - Trying to connect to: msd <http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default> http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default ERROR [Thread-3] (Log.java:197) - Trying to connect to: msd <http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default> http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default [Thread-3] ERROR martconfigurator - Checking exportable ERROR [Thread-3] (Log.java:197) - Checking exportable [Thread-3] ERROR martconfigurator - Done ERROR [Thread-3] (Log.java:197) - Done <ATT00004..gif> Thanks Yue
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