Adding dictybase to oracle VM

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Revision as of 14:57, 11 June 2007 (edit)
E-just@northwestern.edu (Talk | contribs)
(DBD::Oralce)
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Current revision (14:58, 11 June 2007) (edit)
E-just@northwestern.edu (Talk | contribs)
(=Swish-e)
 
Line 159: Line 159:
sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_all sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_all
-==Swish-e=+=Swish-e=
# swish-e 2.4.3 gave the following error in the apache logs: # swish-e 2.4.3 gave the following error in the apache logs:
# symbol lookup error: /usr/lib/perl5/auto/SWISH/API/API.so: undefined symbol: SwishErrorsToStderr # symbol lookup error: /usr/lib/perl5/auto/SWISH/API/API.so: undefined symbol: SwishErrorsToStderr

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Contents

Background and setup

All of the install will be run as the default 'ubuntu' user as of now. In order to be able to use the oracle installed libraries in perl I had to do a rather drastic change of permissions on the whole oracle directory:

su - oracle
chmod -R 755 /oracle/10g

Install required software

  sudo apt-get install cvs

  # checkinstall is for creating deb packages usesd by apt-get
  sudo apt-get install checkinstall

  # dpkg-dev provides tools for for creating a local apt-get repository (where we will put stuff that ubuntu doesn't keep)
  sudo apt-get install dpkg-dev

  # the apache web server
  sudo apt-get install apache2

  # need libxml-simple perl to parse config file in dicty/install/Config
  sudo apt-get install libxml-simple-perl

  # need libmodule-build-perl to install bioperl
  sudo apt-get install libmodule-build-perl

  # need libio-string-perl to install bioperl
  sudo apt-get install libio-string-perl

  #need for installing Net::SSH
  sudo apt-get install libssl-dev

  #need for Bio::Das
  sudo apt-get install libhtml-parser-perl
  sudo apt-get install libwww-perl

  # need for swish-e api
  sudo apt-get install swish-e

  # need for swish-e api
  sudo apt-get install libdbi-perl


  • need libio-string-perl to install bioperl
 cvs login
 cvs checkout dicty/install
 cvs checkout dicty/lib
 cvs checkout dicty/bin
 cvs checkout dicty/build
 cvs checkout dicty/www_dictybase
 cvs checkout dicty/data
 cvs update -r linux_2-0 dicty/install/Config
 cd dicty/install/Config
 perl config.pl
 sudo perl apache_config.pl
 cd ~
 mdkir perl_downloads
 cd perl_downloads

Module::Build

 wget http://search.cpan.org/CPAN/authors/id/K/KW/KWILLIAMS/Module-Build-0.2808.tar.gz
 tar -xvzf Module-Build*.tar.gz
 cd Module-Build*
 perl Makefile.PL
 make
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make install
 #for description, enter Module-Build
 # edit Version, set to 0.2808

Bioperl

 wget http://bioperl.org/DIST/current_core_unstable.zip
 unzip current_core_zip
 cd bioperl-1.52*
 perl Build.PL
 # do not install optional packages
 sudo checkinstall -D --pakdir ~/dicty/install/aptget ./Build install
 #name: libbioperl-perl
 #version 1.52_102
 # arch all

Bioperl Run

 wget http://bioperl.org/DIST/current_run_unstable.zip
 unzip current_run_zip
 cd bioperl-run-1.52*
 # edit Build.PL (add create_packlist=>0 argument to new Module::Build)
 perl Build.PL
 # do not install optional packages
 sudo checkinstall -D --pakdir ~/dicty/install/aptget ./Build install
 #name: libbioperl-run-perl
 #version 1.5.2_102
 # arch all
 sudo checkinstall -D --pakdir ~/dicty/install/aptget ./Build install

libssh2

 wget http://superb-east.dl.sourceforge.net/sourceforge/libssh2/libssh2-0.14.tar.gz
 tar -xvzf libssh2-0.14.tar.gz
 cd Net-SSH2*
 ./configure
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make all install
 # set Name libssh2
 # version 0.14

Net::SSH

 wget http://search.cpan.org/CPAN/authors/id/D/DB/DBROBINS/Net-SSH2-0.10.tar.gz
 tar -xvzf Net-SSH2-0.10.tar.gz
 cd Net-SSH*
 perl Makefile.PL
 make 
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_install

Gbrowse for Oracle Libs

 # Need to have bioperl installed first
 cd dicty/source/Generic-Genome-Browser
 perl Makefile.PL
 # answer questions
 make
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make install_perl

Chado::AutoDBI (GMOD-Oracle)

 # Need to have bioperl installed first
 cd dicty/source/schema/chado
 export GMOD_ROOT=/home/ubuntu/gmod
 perl Makefile.PL
 # answer questions
 make
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_install

Bio::Das

 # need to have installed:
 #  libhtml-parser-perl
 #  libwww-perl
 wget http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-Das-1.03.tar.gz
 tar -xvzf Bio-Das*.*
 cd Bio-Das*
 perl Makefile.PL
 # need pure_install to prevent conflict with perllocal.pod
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_install

Data::Stag

 wget http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/Data-Stag-0.10.tar.gz
 tar -xvzf Data-Stag*.gz
 cd Data-Stag*
 perl Makefile.PL
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_install

DBD::Oralce

 wget http://search.cpan.org/CPAN/authors/id/P/PY/PYTHIAN/DBD-Oracle-1.19.tar.gz
 tar -xvzf DBD-Oracle*.gz
 cd DBD-Oracle*
 export ORACLE_HOME=/oracle/10g
 sudo perl Makefile.PL
 sudo make
 # here we use pure_all because of an error installing with perllocal.pod being installed
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_all

Swish-e

 # swish-e 2.4.3 gave the following error in the apache logs:
 #  symbol lookup error: /usr/lib/perl5/auto/SWISH/API/API.so: undefined symbol: SwishErrorsToStderr
 # had to donwload and install version 2.4.5
 wget http://search.cpan.org/CPAN/authors/id/M/MS/MSCHILLI/SWISH-API-Common-0.03.tar.gz
 tar -xvzf SWISH-API*.gz
 cd SWISH-API*
 sudo perl Makefile.PL
 sudo make
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make install

Swish-e perl API

 # In the swish-e directory created above
 mv perl swish-api
 sudo perl Makefile.PL
 sudo make
 sudo checkinstall -D --pakdir ~/dicty/install/aptget make pure_install

Create apt-get repository for things not in public repositories

  • downloaded liblist-compare-perl from packages.debian.org
  • downloaded libclass-base-perl from packags.debian.org
  • copy both deb files to dicty/install/aptget
 cd dicty/install/aptget/
 dpkg-scanpackages . /dev/null | gzip -9c >Packages.gz
 sudo vi /etc/apt/sources.list
 # add following line (without the '#')
 # deb file:/home/ubuntu/dicty/install/aptget /
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