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
>
> > > --
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