3 bioperl-run INSTALLATION
6 INSTALL THE RIGHT BIOPERL
8 You need at least the corresponding version of Bioperl. Since this
9 is bioperl-run 1.5.2, you will need bioperl 1.5.2.
14 Installation instructions at the following address apply here:
15 http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
16 The next 2 sections summarize the essential points from there.
21 To install using CPAN you will need a recent version (v1.8802 has
22 been tested) of it and your prefer_installer conf set to 'MB':
25 cpan>o conf prefer_installer MB
29 Find the name of the bioperl-run version you want:
33 Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
34 Distribution S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz
38 cpan>install S/SE/SENDU/bioperl-run-1.5.2_100.tar.gz
40 If you've installed everything perfectly then you may pass all the tests
41 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 S/SE/SENDU/bioperl-run-1.5.2_100.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.
59 Download the bioperl-run archive, then extract its contents. Example:
61 >gunzip bioperl-run-<release-version>.tar.gz
62 >tar xvf bioperl-run-<release-version>.tar
65 where <release-version> is the current release.
67 Issue the following command from within bioperl-run/:
71 You can run regression tests and install bioperl-run using the
77 NOTE: many tests will be skipped without the necessary environment
78 variables set to tell Bioperl where your programs are installed.
81 INSTALLING bioperl-run ON WINDOWS
83 The following page on the BioPerl website has up-to-date
84 instructions on how to install bioperl-run on Windows:
86 http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
88 (the instructions are aimed at bioperl-core, but apply
89 equally to bioperl-run)
94 Some important environment variables you need to be aware of.
96 Variable Values Comment
97 --------------------------------------------------------------------
98 PHYLIPVERSION 3.5, 3.6 If you want to run Phylip3.6 you
99 need to set this env variable to 3.6
101 BLASTDIR DIR PATH Point to the directory where BLAST
104 GENSCAN_DIR DIR PATH Point to the directory where
105 HumanIso.smat file is installed
107 EPONINEDIR DIR PATH Point to the directory where
108 eponine_scan.jar is installed
110 PAMLDIR DIR PATH Point to directory where PAML is
113 Generally the all-caps program name concatenated to 'DIR' patten for
114 environment variable names is followed for most programs. However
115 there are some exceptions (some require an underscore between the
116 program name and 'DIR'), so check the documentation for the module
117 you're interested in using.
119 Note that for some programs, having the executables in your path is
120 not enough - the correct environment variable still needs to be set,
121 and sometimes it shouldn't point to the executable location, but
122 somewhere else - again, check the documentation.