TPP:Installing on Ubuntu 8.10

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Revision as of 23:27, 26 December 2008

TPP 4.1.1 @ Ubuntu 8.10 (intrepid)

Recently, my desktop OS is reinstalled with Ubuntu 8.10. This is the log which I made during re-installing TPP. Although I don't use TPP web interface, I will post apache2 setting(without compile) here soon. Of course, if you know, feel free to append it. -- Tkwon 15:27, 26 December 2008 (PST)

Requirement

• Install required packages.

  $ sudo apt-get install 'package-name'

  • build-essential(11.4)
  • libgd2-xpm(2.0.36~rc1~dfsg-3ubuntu1)
  • libgd2-xpm-dev (2.0.36~rc1~dfsg-3ubuntu1)
  • libpng12-dev (1.2.27-1)
  • zlib1g-dev (1:1.2.3.3.dfsg-12ubuntu1)
  • libexpat1-dev (2.0.1-4)
  • gnuplot (4.2.3-1)
  • swig (1.3.35-4ubuntu1)
  • libperl-dev (5.10.0-11.1ubuntu2.2)
• Install libboost packages. I succeeded with 1.34 version.

$ dpkg -l libboost* | grep ii | gawk '{print $2"\t"$3}'
libboost-date-time-dev  1.34.1-11ubuntu1
libboost-date-time1.34.1        1.34.1-11ubuntu1
libboost-dev    1.34.1-11ubuntu1
libboost-doc    1.34.1-11ubuntu1
libboost-filesystem-dev 1.34.1-11ubuntu1
libboost-filesystem1.34.1       1.34.1-11ubuntu1
libboost-graph-dev      1.34.1-11ubuntu1
libboost-graph1.34.1    1.34.1-11ubuntu1
libboost-iostreams-dev  1.34.1-11ubuntu1
libboost-iostreams1.34.1        1.34.1-11ubuntu1
libboost-program-options-dev    1.34.1-11ubuntu1
libboost-program-options1.34.1  1.34.1-11ubuntu1
libboost-python-dev     1.34.1-11ubuntu1
libboost-python1.34.1   1.34.1-11ubuntu1
libboost-regex-dev      1.34.1-11ubuntu1
libboost-regex1.34.1    1.34.1-11ubuntu1
libboost-serialization-dev      1.34.1-11ubuntu1
libboost-serialization1.34.1    1.34.1-11ubuntu1
libboost-signals-dev    1.34.1-11ubuntu1
libboost-signals1.34.1  1.34.1-11ubuntu1
libboost-test-dev       1.34.1-11ubuntu1
libboost-test1.34.1     1.34.1-11ubuntu1        
libboost-thread-dev     1.34.1-11ubuntu1
libboost-thread1.34.1   1.34.1-11ubuntu1
libboost-wave-dev       1.34.1-11ubuntu1
libboost-wave1.34.1     1.34.1-11ubuntu1

• g++ 4.3 is not compatible with current TPP version (and some other extern/ packages, such as tandem/). However, it is the default compiler on intrepid. To remove errors/warnings, I changed default g++ version to g++ 4.2.
  • Install g++ 4.2 using package manager (dselect, etc)
  • Check '/usr/bin/g++'. If it is a symbolic link to g++-4.3, change it to g++-4.2

$ ls -l /usr/bin/g++
lrwxrwxrwx 1 root root 7 2008-06-13 23:08 /usr/bin/g++ -> g++-4.3
$ sudo rm /usr/bin/g++
$ sudo ln -s /usr/bin/g++-4.2 /usr/bin/g++
$ ls -l /usr/bin/g++
lrwxrwxrwx 1 root root 7 2008-06-13 23:08 /usr/bin/g++ -> g++-4.2

Procedure

• Download TPP from http://voxel.dl.sourceforge.net/sourceforge/sashimi/TPP_4-1-1-src.zip. Unzip it.
• Move to src/ directory.

   $ cd trans_proteomic_pipeline/src 

• Make 'Makefile.config.incl' file as follows. PERL_LIB and PERL_LIB_CORE is not configured properly, so you need to set them up manually.

TPP_ROOT=/usr/local/tpp41/
TPP_WEB=/tpp41/
PERL_LIB_CORE= /usr/lib/perl/5.10/CORE/
PERL_LIB=/usr/lib/libperl.a 

• 'make configure' is not working on linux. Jump into 'make all' directly.

 $ make install 

• Copy executable files to TPP_ROOT. 'sudo' is not working, so you need to change the permission of TPP_ROOT manually. Then, 'make install' will work.

$ sudo mkdir /usr/local/tpp41/
$ sudo chown -R <your id> /usr/local/tpp41/
$ make install