[Bioperl-l] A procedure for efficient testing of the installation of BioPerl

Conrad Halling chhalling at verizon.net
Mon Nov 27 22:25:00 EST 2006


I have devised the following procedure that lets me repeatedly install 
BioPerl release candidates for testing the installation process. I am 
performing these tests under Mac OS X 10.4.8. I thought it would be 
useful to document this process for anyone else who is testing the 
installation process.

I downloaded the tarball for Perl 5.8.8 and ran the following commands 
to set up the code for installation:

 cd /Volumes/CHHalling/Perl/Perl-5.8.8
 tar -xzf perl-5.8.8.tgz
 cd perl-5.8.8
 sh Configure -Dprefix=/test/perl -Dcc=gcc -des
 make
 make test

For each round of testing, I run the following commands to install a 
fresh copy of Perl 5.8.8 and then initialize the cpan utility:

 cd /Volumes/CHHalling/Perl/Perl-5.8.8/perl-5.8.8
 sudo rm -rf /test
 sudo mkdir /test
 sudo make install
 sudo rm -rf ~/.cpan
 export PATH=/test/perl/bin:$PATH
 sudo cpan

Then I run my cpan commands. For installing BioPerl without having 
installed the dependencies, I enter the command:

 cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz

For installing the dependencies, then installing BioPerl, I enter the 
commands:

 cpan> install Bundle::BioPerl
 cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz

For testing modifications to Bundle::BioPerl (the subject of my next 
post), I execute the following commands (which exit the cpan utility 
after I have initialized it, create the Bundle subdirectory, copy the 
BioPerl.pm file that contains the Bundle::BioPerl package to the 
.cpan/Bundle directory, start the cpan utility, and install 
Bundle::BioPerl and BioPerl 1.5.2 RC5):

 cpan> exit
 $ sudo mkdir ~/.cpan/Bundle
 $ sudo cp /Volumes/CHHalling/Perl/BioPerl/BioPerl.pm ~/.cpan/Bundle/
 $ sudo cpan
 cpan> install Bundle::BioPerl
 cpan> install S/SE/SENDU/bioperl-1.5.2_005-RCb.tar.gz

When I have finished testing the installation, I loop back to step 2, 
where I remove the /test directory and reinstall Perl 5.8.8.

A note: I was going to use the same procedure to test installing BioPerl 
1.5.2 under Perl 5.6.1, but I discovered that Perl 5.6.1 is *so old* 
that there is no Makefile for Mac OS X.

-- 
Conrad Halling
chhalling at verizon.net



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