Hi Brian, It looks like you have worked through this already. But, just for completeness, any path or setting that you specify in the tpp_gui_config.pl file completely overrides whatever is in tpp_gui.pl, so that there is never a need to edit the latter file. These changes are also not overridden when you upgrade to a newer version of TPP (as long as you don't overwrite the config file). Cheers, --Luis
On Wed, Feb 29, 2012 at 8:35 AM, Brian Hampton <[email protected]> wrote: > So which is better to do, change the specification in the tpp_gui.pl > from: > > my $data_dir = readconfig('data_dir',"${www_root}ISB/ >> data/"); # full path to data directory top-level > > to: > > my $data_dir = readconfig('data_dir',"${www_root}/ >> data/"); # full path to data directory top-level > > Or just change the directory structure to match the former? > > Brian > > On Feb 6, 10:07 am, sirlark <[email protected]> wrote: >> Hi Luis, >> >> Thanks for the heads up. It never occurred to me to look in cgi-bin >> for the config files, I was looking for them in etc. Either way, I >> have it working now, although for the sake of others with similar >> problems, I should point out that I needed to add an extra line, and >> modify your config slightly. This is what I ended up using >> >> 'base_dir' => '/usr/local/apps/tpp/', >> 'www_root' => '/usr/local/apps/tpp/', >> 'data_dir' => '/usr/local/apps/tpp/data/', >> >> Without the 'data_dir' entry, using your config settings, I still kept >> getting the "Attempt to access forbidden directory" error message, and >> I noted that the directory kept getting rewritten to "/usr/lcoal/apps/ >> tpp/ISB/data". A little digging around in tpp_gui.pl showed up this >> line >> >> my $data_dir = readconfig('data_dir',"${www_root}ISB/ >> data/"); # full path to data directory top-level >> >> which clearly defaults to adding ISB to whatever you set as www_root. >> I tried adding a symlink to . in /usr/local/apps/tpp called ISB, but >> petunia seems to resolve out symlinks to determine absolute paths >> (presumably a security mechanism), meaning that visiting /usr/local/ >> apps/tpp/ISB/data got resolved to /usr/local/apps/tpp/data, which was >> not in ISB as per the data_dir default. So I overrode the default in >> tpp_gui_config.pl >> >> Just a gotcha others might come across, hope this helps. >> >> Thanks for the help, >> James >> >> On Feb 1, 11:58 pm, Luis Mendoza <[email protected]> >> wrote: >> >> >> >> >> >> >> >> > Hello James, >> > The error message that you report is generated by Petunia (the user >> > interface) and not the web server. As a measure of precaution, >> > Petunia only allows access to directories below a certain hierarchy, >> > which can be specified when you install the software. >> >> > In order to make these change (which won't be overridden when you >> > upgrade to a newer version of TPP), open the tpp_gui_config.pl file, >> > and add the following lines after the line "# SET TPP_GUI DEFAULTS >> > HERE": >> >> > 'base_dir' => '/usr/local/apps/tpp/', >> > 'www_root' => '/usr/local/apps/tpp/data/', >> >> > Make sure you include the trailing commas and preserve the quotes. >> > You can adjust these values, as necessary, as well as others. You can >> > override other default values in Petunia that are specified by the >> > "readconfig" assignments; look through the first couple of dozen lines >> > of tpp_gui.pl to view them all. On your next upgrade, just remember >> > to copy this file over to preserve your changes. >> >> > Hope this helps, and thanks for using the tools. >> > --Luis >> >> > On Fri, Jan 27, 2012 at 12:13 AM, sirlark <[email protected]> wrote: >> > > Hi, >> >> > > I'm trying to install TPP on Ubuntu Lucid 10.04.3. I had the previous >> > > version (4.4 Vuvuzela) sort of working, that is I could select files >> > > without error, but the results were always empty. This included the >> > > demo data set following the tutorial instructions. I though I would >> > > reinstall from scratch to see if I could get it working, and whilst I >> > > was at it, to get the latest version (TPP v4.5 RAPTURE rev 1, Build >> > > 201201261618 (linux)). The steps I followed were >> >> > > 1. sudo su to root >> > > 2. moved old installtion directory of tpp from /usr/local/apps/tpp to / >> > > usr/local/apps/tpp-4.4 >> > > 3. change into the trans_proteomic_pipeline/src directory >> > > 4. create Makefile.config.incl >> > > 5. change TPP_ROOT in Makefile.config.incl to /usr/local/apps/tpp >> > > 6. make >> > > 7. make install >> > > 8. created /usr/local/apps/tpp/data, and set ownership to www-data:www- >> > > data and permissions to 0770 >> >> > > I didn't make any changes to my apache config assuming it would still >> > > be correct for the version of TPP which ended up in the same directory >> > > as the previous one. Indeed, I can log in to petunia without issue. >> > > But whenever I need to select file for any purposes, I get the >> > > "Attempted to access forbidden directory" message. I have tried >> > > setting everything in /usr/local/apps/tpp to ownership www-data:www- >> > > data, without any noticeable effect. >> >> > > Once I sort this out, I'd be happy to draw up step by step >> > > instructions for installation on Ubuntu, and update the wiki >> > > appropriately, which leads me to an aside question. Will TPP work with >> > > boost-1.4, and if so, which boost libraries does it actually need. >> > > This might make life a lot easier for ubuntu users, since boost-1.4 >> > > libs are in the repos. >> >> > > Thanks, >> > > James >> >> > > -- >> > > You received this message because you are subscribed to the Google >> > > Groups "spctools-discuss" group. >> > > To post to this group, send email to [email protected]. >> > > To unsubscribe from this group, send email to >> > > [email protected]. >> > > For more options, visit this group >> > > athttp://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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