On 16-May-08, at 9:59 AM, Renato Golin wrote:
Hi Renato,
I am sure someone will get back to you with more detailed explanations
but
just want to point out that our docs (e.g.
http://www.biomart.org/install-overview.html)
do actually mention a java version (under "Installing Martj")
"martj has been tested with Java 1.3, 1.4 and 1.5"
and the requirement for apxs to be installed (under "Apache
installation for MartView"):
"The Perl API and MartView configuration scripts check which Apache
modules are available by using apxs (Apache 1.3/1.4) or apxs2 (Apache
2.0+). It requires this tool to live in the same location as the
Apache binary (usually called apache, apache2, or httpd). If you have
installed a binary distribution of Apache, you may also need to
install the Apache development tools to make apxs/apxs2 available"
or did I misunderstand the problems you are reporting?
a.
Hi Mart devs,
I'm installing BioMart (Perl and Java stuff) for UniProt and I
thought would be good to post my progress and the problems I had. As
I have no previous knowledge on BioMart would be good to get a clear
picture on what BioMart looks like to the lay people.
Environment:
(heavily hacked) Ubuntu, current version 8.04
1st. Getting the code
Got the HEAD code from CVS (updated when you sent the email about
0.7 out). Quite easy and good to keep getting changes as CVS
directories remember repository so just run 'cvs up' once in a while.
2nd. "Compiling" the Java code
On martj directory I ran:
$ ant build
First with Java 1.6, broken, than with Java 1.5, smooth.
3rd. Building Perl API and MartView:
$ perl bin/configure.pl -r conf/registryURLPointer.xml
typed 'n' and APIs were built without errors. (Are they on lib/
BioMart?) You could print a usage message like where they are, where
to find the user documents and examples, etc.
Than I changed conf/settings.conf to:
[httpdSettings]
apacheBinary=/usr/sbin/apache2
serverHost=sbornia.homelinux.net
port=9002
proxy=
location=biomart
sbornia is my machine name and it's on DynDns, so no problems there.
than ran:
$ perl bin/configure.pl -r conf/registryURLPointer.xml
and I got some problems...
- First, it found my Apache binary but didn't get my httpd.conf
right, so everything that depended on it screw up, see the error
messages:
Use of uninitialized value in string ne at /home/renato/workspace/
biomart-perl/bin/configureBioMart.pl line 110.
Use of uninitialized value in regexp compilation at /home/renato/
workspace/biomart-perl/bin/configureBioMart.pl line 112.
It should first test to see if the file exists, ask the user if it
doesn't or let me change in the config file right below the binary
setting.
- APXS is needed but not checked nor in configuration:
Got usable Apache in /usr/sbin/apache2, probing for version &
ModPerl configuration
Can't exec "/usr/sbin/apxs2": No such file or directory at /home/
renato/workspace/biomart-perl/bin/configureBioMart.pl line 173.
Use of uninitialized value in scalar chomp at /home/renato/workspace/
biomart-perl/bin/configureBioMart.pl line 174.
Use of uninitialized value in concatenation (.) or string at /home/
renato/workspace/biomart-perl/bin/configureBioMart.pl line 176.
I had the binary installed but it was on /usr/bin instead of /usr/
sbin as apache2 was. It should be in the same basic configuration on
settings.conf.
Got that far today, will post more as I progress...
cheers,
--renato
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