Hi TJ, I tried this and it resulted in a "http error 503 service_unavailable". I went through the logs and determined that there was a missing jar file. I downloaded and added jaxb-xjc-2.1.7.jar and this fixed the issue. Now I need to deal with setting up the page and configuring the login.
Thanks, Iry From: <Esposito>, Anthony <[email protected]<mailto:[email protected]>> Date: Tuesday, January 22, 2013 2:24 PM To: Iry Witham <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: RE: HTTP ERROR: 404 I think I’ve seen this error either when BM tried to start when Apache or something else is already running on the specified port. Make sure dist/biomart.properties (and the file it’s sourced from, conf/files/biomart.properties) are filled out and also make sure there aren’t any trailing spaces at the ends of the http.xxxx lines, e.g.: Oh yes and make sure nothing else is running or listening on whatever port you’re trying to use. ################################################## # HTTP SETTINGS ################################################## http.host = biomart.something.com http.port = 8080 http.url = http:// biomart.something.com:8080/ -- or -- ################################################## # HTTP SETTINGS ################################################## http.host = biomart.something.com http.port = 80 http.url = http:// biomart.something.com/ tj _____ T.J. Esposito Please consider the environment before printing email. From: [email protected]<mailto:[email protected]> [mailto:[email protected]] On Behalf Of Iry Witham Sent: Tuesday, January 22, 2013 10:27 AM To: [email protected]<mailto:[email protected]> Subject: [BioMart Users] HTTP ERROR: 404 I have been able setup a local biomart, but can't get it to display in the browser. I get an HTTP ERROR:404 Problem accessing /.Reason: NOT_FOUND When I run: ./biomart-server.sh check this is what I see for results: Checking arguments to BioMart: BIOMART_HOME = ../dist BIOMART_RUN = ../dist BIOMART_PID = ../dist/biomart.pid BIOMART_CONSOLE = /dev/console BIOMART_PORT = JAVA_OPTIONS = -Dbiomart.properties=../dist/biomart.properties -Xmx2048m JAVA = /usr/bin/java CLASSPATH = RUN_CMD = /usr/bin/java -cp "../dist/scripts/biomart-start.jar:../dist/lib/abbot.jar:../dist/lib/activation.jar:../dist/lib/ant4eclipse.jar:../dist/lib/ant-launcher.jar:../dist/lib/aopalliance.jar:../dist/lib/arq-2.8.7.jar:../dist/lib/asm-3.1.jar:../dist/lib/batik-anim.jar:../dist/lib/batik-awt-util.jar:../dist/lib/batik-css.jar:../dist/lib/batik-dom.jar:../dist/lib/batik-ext.jar:../dist/lib/batik-gui-util.jar:../dist/lib/batik-gvt.jar:../dist/lib/batik-parser.jar:../dist/lib/batik-svg-dom.jar:../dist/lib/batik-svggen.jar:../dist/lib/batik-util.jar:../dist/lib/batik-xml.jar:../dist/lib/biomart-0.8.jar:../dist/lib/biomart-string2longset.jar:../dist/lib/bsh-2.0b4.jar:../dist/lib/colt-1.2.0.jar:../dist/lib/commons-beanutils-1.7.jar:../dist/lib/commons-codec-1.3.jar:../dist/lib/commons-collections.jar:../dist/lib/commons-dbcp-1.2.2.jar:../dist/lib/commons-fileupload-1.2.1.jar:../dist/lib/commons-httpclient-3.0.1.jar:../dist/lib/commons-io-1.4.jar:../dist/lib/commons-lang.jar:../dist/lib/commons-logging-1.1.1.jar:../dist/lib/commons-pool-1.5.2.jar:../dist/lib/core-3.1.1.jar:../dist/lib/costello.jar:../dist/lib/db2jcc4.jar:../dist/lib/dna-common-0.6.jar:../dist/lib/dsn.jar:../dist/lib/ecp1_0beta.jar:../dist/lib/ensj.jar:../dist/lib/ensj-util.jar:../dist/lib/epsgraphics2d.jar:../dist/lib/ezmorph.jar:../dist/lib/gmbal-api-only.jar:../dist/lib/gnu-regexp-1.1.0.jar:../dist/lib/guava-r09.jar:../dist/lib/guice-2.0.jar:../dist/lib/guicemanaged-0.4.jar:../dist/lib/guice-servlet-2.0.jar:../dist/lib/httpclient-4.0.jar:../dist/lib/httpcore-4.0.1.jar:../dist/lib/icgc.jar:../dist/lib/icu4j-3.4.4.jar:../dist/lib/idw-gpl.jar:../dist/lib/imap.jar:../dist/lib/iri-0.8.jar:../dist/lib/iText-5.0.4.jar:../dist/lib/jackson-core-asl-1.4.0.jar:../dist/lib/jackson-jaxrs-1.4.0.jar:../dist/lib/jackson-mapper-asl-1.4.0.jar:../dist/lib/jackson-xc-1.4.0.jar:../dist/lib/jai_imageio.jar:../dist/lib/java-getopt-1.0.9.jar:../dist/lib/jaxb-api.jar:../dist/lib/jaxb-impl.jar:../dist/lib/jaxws-api.jar:../dist/lib/jaxws-rt.jar:../dist/lib/jcommon-1.0.16.jar:../dist/lib/jconsole.jar:../dist/lib/jdbc2_0-stdext.jar:../dist/lib/jdom-1.0.jar:../dist/lib/je-4.0.103.jar:../dist/lib/jena-2.6.4.jar:../dist/lib/jena-2.6.4-tests.jar:../dist/lib/jersey-bundle-1.4-SNAPSHOT.jar:../dist/lib/jersey-guice-1.4.jar:../dist/lib/jetty-6.1.23.jar:../dist/lib/jetty-j2se6-6.1.26.jar:../dist/lib/jetty-session-ext.jar:../dist/lib/jetty-setuid-6.1.23.jar:../dist/lib/jetty-util-6.1.23.jar:../dist/lib/jfreechart-1.0.13.jar:../dist/lib/jline.jar:../dist/lib/jopt-simple-3.1.jar:../dist/lib/jsp-2.1-glassfish-9.1.1.B60.25.p2.jar:../dist/lib/jsp-2.1-jetty-6.1.23.jar:../dist/lib/jsp-api-2.1-glassfish-9.1.1.B60.25.p2.jar:../dist/lib/jsr305.jar:../dist/lib/jsr311-api-1.1.1.jar:../dist/lib/jstl-api-1.2.jar:../dist/lib/jstl-impl-1.2.jar:../dist/lib/junit-4.8.2.jar:../dist/lib/jython.jar:../dist/lib/libreadline-java.jar:../dist/lib/lingpipe-3.8.2.jar:../dist/lib/log4j-1.2.15.jar:../dist/lib/lucene-core-2.3.1.jar:../dist/lib/mailapi.jar:../dist/lib/management-api.jar:../dist/lib/mysql-connector-java-5.1.15-bin.jar:../dist/lib/nekohtml-1.9.7.jar:../dist/lib/oauth-java-20100819.jar:../dist/lib/ojdbc5.jar:../dist/lib/opencsv-2.1.jar:../dist/lib/openid4java-0.9.7-SNAPSHOT-20110525-jhsu.jar:../dist/lib/optional.jar:../dist/lib/p6spy.jar:../dist/lib/policy.jar:../dist/lib/pop3.jar:../dist/lib/postgresql-9.0-801.jdbc4.jar:../dist/lib/salma-hayek.jar:../dist/lib/scribe-1.0.3.jar:../dist/lib/servlet-api-2.5.jar:../dist/lib/slf4j-api-1.5.11.jar:../dist/lib/slf4j-nop-1.5.11.jar:../dist/lib/smtp.jar:../dist/lib/sqljdbc4.jar:../dist/lib/stax-api-1.0.1.jar:../dist/lib/stax-ex.jar:../dist/lib/streambuffer.jar:../dist/lib/velocity-1.6.2.jar:../dist/lib/voldemort-0.81.jar:../dist/lib/wstx-asl-3.2.9.jar:../dist/lib/xalan.jar:../dist/lib/xercesImpl.jar:../dist/lib/xml-apis-ext.jar:../dist/lib/xml-apis.jar:../dist/lib/zzNetBoxDependencies.jar:../dist/lib/zzNetBoxModified.jar" -Dbiomart.properties=../dist/biomart.properties -Xmx2048m -Dbiomart.dir=../dist org.biomart.start.Main BioMart running pid=6945 I had suspected to see something listed under 'BIOMART_PORT'. Any suggestions? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
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