3 bioperl-run INSTALLATION
5 INSTALL THE RIGHT BIOPERL
7 You need at least the corresponding version of Bioperl. Since this
8 is BioPerl-run 1.6.1, you should use BioPerl 1.6.
13 Installation instructions at the following address apply here:
14 http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
15 The next 2 sections summarize the essential points from there.
20 To install using CPAN you will need a recent version (v1.8802 has
21 been tested) of it and your prefer_installer conf set to 'MB':
24 cpan>o conf prefer_installer MB
28 Find the name of the bioperl-run version you want:
32 Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
33 Distribution C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
37 cpan>install C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
39 If you've installed everything perfectly then you may pass all the tests
40 run in the './Build test' phase.
42 It's also possible that you may fail some tests. Possible explanations:
43 problems with local Perl installation, previously undetected bug in
44 Bioperl, flawed test script and so on. A few failed tests may not affect
45 your usage of bioperl-run.
47 If you decide that the failed tests will not affect how you intend to use
48 bioperl-run and you'd like to install anyway do:
50 cpan>force install C/CJ/CJFIELDS/BioPerl-run-1.6.1.tar.gz
52 This is what most experienced Bioperl users would do. However, if you're
53 concerned about a failed test and need assistance or advice then contact
54 bioperl-l@bioperl.org.
58 Download the bioperl-run archive, then extract its contents. Example:
60 >gunzip bioperl-run-<release-version>.tar.gz
61 >tar xvf bioperl-run-<release-version>.tar
64 where <release-version> is the current release.
66 Issue the following command from within bioperl-run/:
70 You can run regression tests and install bioperl-run using the
76 NOTE: many tests will be skipped without the necessary environment
77 variables set to tell Bioperl where your programs are installed.
79 INSTALLING bioperl-run ON WINDOWS
81 The following page on the BioPerl website has up-to-date
82 instructions on how to install bioperl-run on Windows:
84 http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
86 (the instructions are aimed at bioperl-core, but apply
87 equally to bioperl-run)
92 Some important environment variables you need to be aware of.
94 Variable Values Comment
95 --------------------------------------------------------------------
96 PHYLIPVERSION 3.5, 3.6 If you want to run Phylip3.6 you
97 need to set this env variable to 3.6
99 BLASTDIR DIR PATH Point to the directory where BLAST
102 GENSCAN_DIR DIR PATH Point to the directory where
103 HumanIso.smat file is installed
105 EPONINEDIR DIR PATH Point to the directory where
106 eponine_scan.jar is installed
108 PAMLDIR DIR PATH Point to directory where PAML is
111 Generally the all-caps program name concatenated to 'DIR' patten for
112 environment variable names is followed for most programs. However
113 there are some exceptions (some require an underscore between the
114 program name and 'DIR'), so check the documentation for the module
115 you're interested in using.
117 Note that for some programs, having the executables in your path is
118 not enough - the correct environment variable still needs to be set,
119 and sometimes it shouldn't point to the executable location, but
120 somewhere else - again, check the documentation.