Hi James,
I indeed forgot to include data_dir as part of my answer; glad that
you found that and got it to work.
And yes, Petunia resolves to absolute path names by default as an
extra measure of security.
Cheers,
--Luis
On Mon, Feb 6, 2012 at 7:07 AM, sirlark <jgdom...@gmail.com> 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 <luis.mend...@systemsbiology.org>
> 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 <jgdom...@gmail.com> 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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