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]] On Behalf Of
Iry Witham
Sent: Tuesday, January 22, 2013 10:27 AM
To: [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
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