Hi Heather, Unfortunately we do not currently officially support proxy servers.
We have tested some arguments on the JVM, but none was reliable enough for us to recommend. We found that only a limited number of proxy servers were easily supported natively on the JVM. You can pass extra JVM arguments to the biomart-server.sh script. E.g. ./scripts/biomart-server.sh start -Dhttp.proxyHost=... -Dhttp.proxyPort=... We are looking at more sophisticated solutions to handle proxy servers in the future. -jack From: "Estrella, Heather" <[email protected]<mailto:[email protected]>> Date: Fri, 2 Sep 2011 13:39:16 -0400 To: BioMart Users <[email protected]<mailto:[email protected]>> Subject: [BioMart Users] Setting proxy servers to get around firewall Has anyone used a proxy server within BioMart to get around an internal firewall? I’ve set the proxy parameters in dist/conf/xml/biomart.all.properties http.proxyHost=proxyserver.com http.proxyPort=8080 I am able to set the http_proxy environment variable and access the external site using curl from the command line, but when I try to run the same query from within BioMart it fails. Error in stdouterror log file: org.biomart.common.exceptions.BioMartException: HTTP Error 404 - <HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;charset=ISO-8859-1"><TITLE>Not Found</TITLE></HEAD> <H1>Not Found</H1> The requested object does not exist on this server. The link you followed is either outdated, inaccurate, or the server has been instructed not to let you have it. My guess is that I’m not setting something correctly in the biomart.all.properties file or there is another setting that I’m missing. If anyone has experience with proxy settings within BioMart, it would be great to get some input fromanyone who has Biomart going through a proxy server. Thanks, Heather
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