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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 1.6.9, you should use BioPerl 1.6.9.
INSTALLATION
Installation instructions at the following address apply here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
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 C/CJ/CJFIELDS/BioPerl-run-1.6.9.tar.gz
Now install:
cpan>install C/CJ/CJFIELDS/BioPerl-run-1.6.9.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 C/CJ/CJFIELDS/BioPerl-run-1.6.9.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
bioperl-l@bioperl.org.
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)
ENVIRONMENT VARIABLES
Some important environment variables you need to be aware of.
Variable Values Comment
--------------------------------------------------------------------
PHYLIPVERSION 3.5, 3.6 If you want to run Phylip3.6 you
need to set this env variable to 3.6
BLASTDIR DIR PATH Point to the directory where BLAST
is installed
GENSCAN_DIR DIR PATH Point to the directory where
HumanIso.smat file is installed
EPONINEDIR DIR PATH Point to the directory where
eponine_scan.jar is installed
PAMLDIR DIR PATH Point to directory where PAML is
installed
Generally the all-caps program name concatenated to 'DIR' patten for
environment variable names is followed for most programs. However
there are some exceptions (some require an underscore between the
program name and 'DIR'), so check the documentation for the module
you're interested in using.
Note that for some programs, having the executables in your path is
not enough - the correct environment variable still needs to be set,
and sometimes it shouldn't point to the executable location, but
somewhere else - again, check the documentation.