> Thanks for the quick response! > >> please refer to docs or you may see the quick install guide >> (http://www.biomart.org/install-overview.html) about how to set your >> conf/settings.conf which contains useful information about your apache >> binary , host, port etc etc. > > Right. I'm following those instructions, but I was sort of expecting to > see "Looks good.... you are done." at the end of step 1.3.4.1. It does > say "Configuration of the Perl API requires a single step". If any of > you guys are involved in this guide, may I suggest adding a few words > along the lines of "if you experience difficulties, please see section > X.Y on how to configure Z"? >
Thanks for your suggestion, we will look into this. >> As you can see in your install attempt, it cant find apache binary and >> subsequently fails on mod_perl and other libraries. > > Check. Fixed it for my platform. It's called apache2 on debian/ubuntu > systems. Now I have this error message instead: You apache doesnt have apxs or apxs2 in the same directory or you dont have it at all. You need apxs or apxs2 (apache extension tool) and help is provided in detailed documentation. you need to have this under same directory as of 'httpd' or create a symlink if its somewhere else. for uninitialised warnings , please uncomment line 83 of bin/configureBioMart.pl and see what gets printed on screen. cheers syed >> $ perl bin/configure.pl -r conf/registryURLPointer.xml >> >> Do you want to install in API only mode [y/n] [n]: >> >> Checking prerequisites ...[Looks good] >> Use of uninitialized value in string ne at >> /media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl >> line 84. >> Use of uninitialized value in regexp compilation at >> /media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl >> line 86. >> >> rm >> /media/sda8/yohell/download/biomart/biomart-perl/conf/templates/default/*.ttcrm: >> cannot remove >> `/media/sda8/yohell/download/biomart/biomart-perl/conf/templates/default/*.ttc': >> No such file or directory >> >> APACHE: /usr/sbin/apache2 >> HOST: localhost >> PORT: 9002 >> PROXY: >> LOCATION: biomart >> >> You can change the above configuration by editing >> "biomart-perl/conf/settings.conf" >> >> >> >> Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl >> configuration >> Can't exec "/usr/sbin/apxs2": No such file or directory at >> /media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl >> line 147. >> Use of uninitialized value in scalar chomp at >> /media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl >> line 148. >> Use of uninitialized value in concatenation (.) or string at >> /media/sda8/yohell/download/biomart/biomart-perl/bin/configureBioMart.pl >> line 150. >> Libdir /media/sda8/yohell/download/biomart/biomart-perl/lib is not in >> @INC, adding to @INC >> >> Processing Cached Registry: >> /media/sda8/yohell/download/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached > > (what's all that "use of uninitialized value" business? It doesn't look > too good, does it?) > > Any suggestions? > /Joel > ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
