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INSTALL
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INSTALL
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bioperl-run INSTALLATION
INSTALL THE RIGHT BIOPERL
You need at least the corresponding version of Bioperl. Since this
is BioPerl-run 1.007001, you should use BioPerl 1.007001.
INSTALLATION
Installation instructions at the following address apply here:
http://bioperl.org/INSTALL.html
The next 2 sections summarize the essential points from there.
CPAN INSTALLATION
To install using CPAN you will need a recent version (v1.8802 has
been tested) of it and your prefer_installer conf set to 'MB':
>cpan
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q
Find the name of the bioperl-run version you want:
>cpan
cpan>d /bioperl-run/
Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
Distribution CJFIELDS/BioPerl-Run-1.007001.tar.gz
Now install:
cpan>install CJFIELDS/BioPerl-Run-1.007001.tar.gz
If you've installed everything perfectly then you may pass all the tests
run in the './Build test' phase.
It's also possible that you may fail some tests. Possible explanations:
problems with local Perl installation, previously undetected bug in
Bioperl, flawed test script and so on. A few failed tests may not affect
your usage of bioperl-run.
If you decide that the failed tests will not affect how you intend to use
bioperl-run and you'd like to install anyway do:
cpan>force install CJFIELDS/BioPerl-Run-1.007001.tar.gz
This is what most experienced Bioperl users would do. However, if you're
concerned about a failed test and need assistance or advice then contact
MANUAL INSTALLATION
Download the bioperl-run archive, then extract its contents. Example:
>gunzip bioperl-run-<release-version>.tar.gz
>tar xvf bioperl-run-<release-version>.tar
>cd bioperl-run
where <release-version> is the current release.
Issue the following command from within bioperl-run/:
>perl Build.PL
You can run regression tests and install bioperl-run using the
following commands:
>./Build test
>./Build install
NOTE: many tests will be skipped without the necessary environment
variables set to tell Bioperl where your programs are installed.
INSTALLING bioperl-run ON WINDOWS
The following page on the BioPerl website has up-to-date
instructions on how to install bioperl-run on Windows:
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
(the instructions are aimed at bioperl-core, but apply
equally to bioperl-run)