Also - BioMart builds its own httpd.conf and does not integrate with any existing Apache installation, if that's what you mean by a broken httpd.conf? On top of that, without apxs, it wouldn't have been able to build it's own httpd.conf anyway.
cheers, Richard 2008/5/16 Arek Kasprzyk <[EMAIL PROTECTED]>: > > 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 >> >> >> -- >> Reclaim your digital rights, eliminate DRM, learn more at >> http://www.defectivebydesign.org/what_is_drm > >
