Dear Natalie and Joe,
thanks a lot for your help and advice - I think that I have managed to
install TPP now. At this stage, I am slightly stuck (don't know
exactly how to configure it, where to put the search engines we are
using here (we have installations of thegpm and mascot) and how to get
data to PeptideProphet, ProteinProphet and the remainder of the family
(I apologise for the naivety of my questions and promise to come back
with more constructive ones, once I understand more).
One thing struck me as a slight inconsistency:
In the installation script it says (in the section about configuring
apache):
---------------------- from 'install-ubuntu-9_04.sh'
---------------------------
# directory to store data for web browser viewing
ScriptAlias /tpp/data "/usr/local/apps/tpp/data"
<Directory "/usr/local/apps/tpp/data">
AllowOverride None
Options Indexes FollowSymLinks Includes
Order allow,deny
Allow from all
</Directory>
# directory for tpp's html resources (css, js, images, etc)
ScriptAlias /tpp/html "/usr/local/apps/tpp/html"
<Directory "/usr/local/apps/tpp/html">
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
# directory for tpp's schema resources
<Directory "/usr/local/apps/tpp/schema">
AllowOverride None
Options Includes Indexes FollowSymLinks MultiViews
Order allow,deny
Allow from all
</Directory>
# directory for tpp's executable files
ScriptAlias /tpp/cgi-bin "/usr/local/apps/tpp/cgi-bin"
<Directory "/usr/local/apps/tpp/cgi-bin">
#AllowOverride AuthConfig Limit
AllowOverride All
Options Indexes FollowSymLinks MultiViews ExecCGI +Includes
AddHandler default-handler .jpg .png .css .ico .gif
AddHandler cgi-script .cgi .pl
Order allow,deny
Allow from all
SetEnv WEBSERVER_ROOT /usr/local/apps
#SetEnv WEBSERVER_ROOT /var/www
</Directory>
------------------------ end -------------------------------------
However, when I look at /usr/local/apps, I see the following
directories:
------------------------ terminal output --------------------------
ac...@linux01:/usr/local/apps$ ll
total 24
drwxr-xr-x 2 root root 4096 2009-08-24 11:13 tpp
drwxr-xr-x 2 root root 4096 2009-08-24 11:13 tppbin
drwxr-xr-x 4 root root 4096 2009-08-24 11:13 tppcgi-bin
drwxr-xr-x 2 root root 4096 2009-08-24 11:13 tppetc
drwxr-xr-x 5 root root 4096 2009-08-24 11:13 tpphtml
drwxr-xr-x 2 root root 4096 2009-08-24 11:13 tppschema
------------------------ end terminal output -------------------
Does this indicate that I have done something wrong during the
installation process or that the file structure might have changed
slightly, without this being reflected in the installation script?
Your help is very much appreciated,
Achim
On Aug 21, 7:11 pm, Natalie Tasman <[email protected]>
wrote:
> Hello Achim,
>
> You will find scripts for installing all required TPP-related packages
> for ubuntu 9.04 in the 4.3.0 installer_linux directory. The 4.2.1
> build instructions don't exactly apply, but should still give you a
> good guide. One big change is that I've now included boost and the
> TPP installer builds that for you. Without configuring directories
> (with an optional Makefile.config.incl file), I routinely do clean
> builds on ubuntu 9.04 to test the build process.
>
> Let me know how it goes,
>
> Natalie
>
> On Aug 21, 2009, at 8:25 AM, Achim wrote:
>
> > Dear all,
>
> > I am trying to install tpp 4.3.0 on ubuntu 9.04, following step by
> > step the beautifully clear instructions for tpp 4.2.1 on the wiki.
>
> > Upon compilation of the tpp I get stuck:
>
> > ---------- output from make -j5 command ----------------
> > ...
> > perl -c -I ../../build/linux ../../build/linux/tpp_gui.pl
> > Can't locate XML/Parser.pm in @INC (@INC contains: ../../build/
> > linux /usr/local/lib/perl5/5.8.8/x86_64-linux /usr/local/lib/
> > perl5/5.8.8 /usr/local/lib/perl5/site_perl/5.8.8/x86_64-linux /usr/
> > local/lib/perl5/site_perl/5.8.8 /usr/local/lib/perl5/site_perl .)
> > at ../../build/linux/tpp_gui.pl line 16.
> > BEGIN failed--compilation aborted at ../../build/linux/tpp_gui.pl
> > line 16.
> > make[2]: *** [../../build/linux/tpp_gui.pl] Error 2
> > make[2]: *** Deleting file `../../build/linux/tpp_gui.pl'
> > make[2]: Leaving directory `/usr/local/src/tpp-4.3.0/src/perl_paths'
> > make[1]: *** [perl_paths] Error 2
> > make[1]: Leaving directory `/usr/local/src/tpp-4.3.0/src'
> > make: *** [default] Error 2
> > ---------- end output -----------------
>
> > When I look for Parser.pm, I find it in the following locations:
> > ----------- copied from terminal -------------
> > find / -name 'Parser.pm' -print
> > /usr/share/perl5/RPC/XML/Parser.pm
> > /usr/share/perl/5.10.0/Pod/Parser.pm
> > /usr/lib/perl5/HTML/Parser.pm
> > /usr/lib/perl5/XML/Parser.pm
> > /usr/local/perl-5.8.8/lib/Pod/Parser.pm
> > /usr/local/lib/perl5/site_perl/5.8.8/x86_64-linux/HTML/Parser.pm
> > /usr/local/lib/perl5/5.8.8/Pod/Parser.pm
>
> > perl -version
>
> > This is perl, v5.8.8 built for x86_64-linux
> > ------------- end copy from terminal -----------
>
> > Anybody's help is very much appreciated.
>
> > Thanks a lot in advance,
>
> > Achim
>
> > --
> > Achim Treumann
> > NEPAF, Newcastle upon Tyne, UK
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