## this is to show the process to load the server for tomcat/ant/postgresql/
http://www.intermine.org/wiki/Prerequisites
Need-- subversion 1,5/ Java SDK / Ant 1.6.5 / Tomcat 5.0 / PostgreSQL 8.3 / JUni 3.8.1 Perl 5.8.8 or above.`
Here seems to be the order of priority this may change at anytime.
1> load the apache ant and tomcat, those are strait forward.
- tar -xvf apache-ant-1.8.2-bin.tar / apache-tomcat-7.0.8.tar
2> Java SDK -- run ./jdk-6u24-linux-x64.bin
3> perl and subversion can be loaded independently
4> JUnit
5> PostgreSQK >>
a) postgresql-libs-8.4.7-1PGDG.rhel5.x86_64.rpm (no dep)
b) postgresql-8.4.7-1PGDG.rhel5.x86_64.rpm (no dep)
c) postgresql-devel-8.4.7-1PGDG.rhel5.x86_64.rpm (no dep)
d) postgresql-server-8.4.7-1PGDG.rhel5.x86_64.rpm (no dep)
## from here on there are lots of dependencies.
e) postgresql-contrib-8.4.7-1PGDG.rhel5.x86_64.rpm needs:
->libossp-uuid.so.15()(64bit)
f) compat-postgresql-libs-4-1PGDG.rhel5.x86_64.rpm needs:
->/usr/lib64/libpq.so.4.1 conflicts with file from postgresql-libs-8.1.23-1.el5_6.1.x86_64
g) postgis-1.3.6-1.rhel5.x86_64.rpm needs:
->/usr/bin/rebuild-gcj-db
->geos
->libgeos_c.so.1()(64bit)
->libproj.so.0()(64bit)
->proj
Downloaded proj-4.5.0-3.el5.x86_64.rpm that listed libproj.so.0 contained.
h)sudo rpm -i proj-4.5.0-3.el5.x86_64.rpm (no dep)
## try postgis again!
h) sudo rpm -i postgis-1.3.6-1.rhel5.x86_64.rpm
## killed tow more dependencies libproj and proj still have:
-> /usr/bin/rebuild-gcj-db
->geos
->libgeos_c.so.1()(64bit)
## found geos-3.0.0-1/fc8.rf.x86_64.rpm says contains:
## load this geos:
i) sudo rpm -i geos-3.0.0-1.fc8.rf.x86_64.rpm needs dep:
->libgeos-3.0.0.so()(64bit)
## wich says it needs dep in libgeos-3.0.0.so()(64bit) which is listed in
## itself??? how does that work?
## found geos-3.0.0-3.el5.kb.x86_64.rpm and the ran with (no dep) NICE!!
## try again:
h) sudo rpm -i postgis-1.3.6-1.rhel5.x86_64.rpm
## that knocked out two more dependencies only /usr/bin/rebuild-gcj-db left!
## searched and found java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64.rpm
J) sudo rpm -i java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64.rpm
Failed dependencies:
/usr/bin/gcj-dbtool is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
/usr/bin/gij is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
/usr/lib64/security/classpath.security is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
jpackage-utils >= 1.7.5-3.10 is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
libgcj >= 4.1.2-5 is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
rpmlib(FileDigests) <= 4.6.0-1 is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
sinjdoc is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
rpmlib(PayloadIsXz) <= 5.2-1 is needed by java-1.5.0-gcj-1.5.0.0-34.fc14.x86_64
## went back to run postgresql-contrib-8.4.7-1PGDG.rhel5.x86_64.rpm and got
## one dep libossp-uuid.so.15. searched and found uuid-1.5.1-3.el5.x86_64.rpm
and ran that:
k) sudo rpm -i uuid-1.5.1-3.el5.x86_64.rpm (no dep)
## now rerun sudo rpm -i postgresql-contrib-8.4.7-1PGDG.rhel5.x86_64.rpm
## ran CLEAN!!! so now postgis needs the rebuild-gcj-db I found it in gjdoc-0.7.7-12.el5.x86_64.rpm
## lets run it and see: sudo rpm -i gjdoc-0.7.7-12.el5.x86_64.rpm
## needs antlr dependency and others ant-antlr-1.7.1-7.jpp5.noarch.rpm
## and run it: needs two more dpendencies found libgcj-4.5.1-4.fc14.i686.rpm
## for dependencies for gjdoc run it: failed dependencies!!!
libgio-2.0.so.0 found glib2-2.28.1-1.fc15.i686.rpm ran it it needed 6 dep!!
looked up again for rhel5 and got zenoss-3.1.0.el5.x86_64.rpm ran it:
had 8 dependencies!!!! going back to libgio dependency and found glib2-2.28.1-1.fc15.x86_64.rpm run it:
many many many more dependencies.....???? must be an easier way???
the only thing stopping this from completing is the rebuild-gcj-db!! and it has so many dependencies on the de
pendencies.. this can't be right.
discovered the uses of yum. ran yum install on some dependencies and it found all of them!!
now it worked!! postgis-1.3.6-1.rhel5.x86_64.rpm ran (no dep) NICE!!! YUM!!
Now the last one is: compat-postgresql-libs-4-1PGDG.rhel5.x86_64.rpm
I tried the yum install and it failed no reason why. says no Public key installed, tried to import the public
key but it did not work still fails.
actually it is not failing it is listing a conflicting file with postgresql-libs not suer if that's even a p
roblem.
#### so I have learned of some dependency work arounds. ####
rpm -ivh --aid package.rpm this will automatically find and load the dependencies.
also put all the rpms together in one dir and run rpm -ivh *rpm and it will automatically run them in order.
also run form yum and yum will install all packages and dependencies privided the public key is correct.
#### final results ######
Tomcat should be set up in /usr/local/tomcat with a link to apache-tomcat-version.
goad> cd /usr/local/
goad> ls
ant apache-tomcat-6.0.32 bin games junit lib64 man share tomcat
apache-ant-1.8.2 apache-tomcat-7.0.8 etc include lib libexec sbin src
### should be a link set up for tomcat and ant ######
lrwxrwxrwx 1 root root 16 Mar 4 16:20 ant -> apache-ant-1.8.2
lrwxrwxrwx 1 root root 20 Mar 7 15:55 tomcat -> apache-tomcat-6.0.32
### http.conf files for apache are here: ###
/usr/local/etc/httpd/conf:
httpd.conf httpd.conf.orig magic
### httpd binary is included in redhat ####
### binary is here: ###
sudo /usr/sbin/httpd -v
Server version: Apache/2.2.3
Server built: Dec 7 2010 11:19:58
### and apachectl ###
sudo /usr/sbin/apachectl
### tomcat index.html files are here: ###
/usr/local/apache-tomcat-6.0.32/webapps/ROOT
### tomcat workers.properties file ###
oad> more /usr/local/apache-tomcat-6.0.32/conf/workers.properties
# The workers that your plugins should create and work with
#
worker.list=test,prod
#
# Defining a worker named test and of type ajp13
#
worker.test.port=8009
worker.test.host=test.stanford.edu
worker.test.type=ajp13
#
# Defining a worker named prod and of type ajp13
#
worker.prod.port=8019
worker.prod.host=goad.stanford.edu
worker.prod.type=ajp13
### tomcat startup is here ###
/usr/local/apache-tomcat-6.0.32/bin/startup.sh
NOTE ---> the tomcat would not start it failed because of variable sets
that it could not resolve: Turns out in the release they don't have
the setenv.sh file. It was on celis but not goad. So it failed.
I added this file to the startup.sh directory and it started.
Here is how it looks:
goad> more setenv.sh
PATH=/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin:/bin:/sbin:/usr/java/default/bin:/usr/local/ant/bin
export PATH
TOMCAT_OWNER=tomcat
TOMCAT_OPTS='-Xmx256m -Xms128m'
export TOMCAT_OPTS
JAVA_OPTS=${TOMCAT_OPTS}
export JAVA_OPTS
CATALINA_HOME=/usr/local/tomcat
export CATALINA_HOME
CATALINA_BASE=$CATALINA_HOME
export CATALINA_BASE
BASEDIR=$CATALINA_HOME
export BASEDIR
JAVA_HOME=/usr/java/default
export JAVA_HOME
CLASSPATH=${CLASSPATH}:${CATALINA_HOME}/lib:${CATALINA_HOME}/classes:${CATALINA_HOME}/bin/tomcat-juli.jar:${CA
TALIN
A_HOME}/bin/bootstrap.jar:/usr/local/javaclass:/usr/local/apache-tomcat-6.0.29-src/output/build/webapps/exampl
es/WE
B-INF/classes:${CATALINA_HOME}/lib/annotations-api.jar:${CATALINA_HOME}/lib/catalina-ant.jar:${CATALINA_HOME}/
lib/c
atalina-ha.jar:${CATALINA_HOME}/lib/catalina.jar:${CATALINA_HOME}/lib/catalina-tribes.jar:${CATALINA_HOME}/lib
/el-a
pi.jar:${CATALINA_HOME}/lib/jasper-el.jar:${CATALINA_HOME}/lib/jasper.jar:${CATALINA_HOME}/lib/jasper-jdt.jar:
${CAT
ALINA_HOME}/lib/jsp-api.jar:${CATALINA_HOME}/lib/servlet-api.jar:${CATALINA_HOME}/lib/tomcat-coyote.jar:${CATA
LINA_
HOME}/lib/tomcat-dbcp.jar:${CATALINA_HOME}/lib/tomcat-i18n-es.jar:${CATALINA_HOME}/lib/tomcat-i18n-fr.jar:${CA
TALI
NA_HOME}/lib/tomcat-i18n-ja.jar
### tomcat also failed for the jdk (java) files would not work ###
### I had to move alll the files and JD dir to /usr/java and link the ###
### the jdk dir to default so that tomcat can find it. and the JRE link ex:
### and link the /usr/java/jdk1.6.0_24 to latest ###
goad> cd /usr/java
goad> ls -l
total 4
lrwxrwxrwx 1 root root 11 Mar 8 16:37 default -> jdk1.6.0_24
drwxr-xr-x 10 admin admin 4096 Mar 8 16:38 jdk1.6.0_24
lrwxrwxrwx 1 root root 15 Mar 8 16:37 jre -> jdk1.6.0_24/jre
lrwxrwxrwx 1 root root 21 Mar 9 15:07 latest -> /usr/java/jdk1.6.0_24
### starting the httpd apache webserver ###
goad>sudo /usr/sbin/apachectl configtest
Syntax OK
sudo /usr/sbin/httpd -k start