BP_NETINSTALL(1p) User Contributed Perl Documentation BP_NETINSTALL(1p)NAME
bp_netinstall.pl
SYNOPSIS
bp_netinstall.pl -b|--build_param_str BUILD_STRING [options]
options:
-h|--help Show this message
-d|--dev Use the development version of bioperl from git
--build_param_str=<args> Parameters that are passed in at 'perl Build.PL'
--install_param_str=<args>
Use this string to predefine './Build install'
parameters such as 'install_base' for
bioperl installation
--bioperl_path Path to BioPerl tarball (will not download BioPerl)
--skip_start Don't wait for 'Enter' at program start
DESCRIPTION
Net-based installer of BioPerl; this is based on the GBrowse netinstaller and hopefully all references to GBrowse have been removed. Let
me know if not.
Save this to disk as "bp_netinstall.pl" and run:
[sudo] perl bp_netinstall.pl
AUTHOR
Scott Cain scain@cpan.org
COPYRIGHT
2010. This script may be distributed under the same license as perl.
perl v5.14.2 2012-03-02 BP_NETINSTALL(1p)
Check Out this Related Man Page
Bio::TreeIO::NewickParser(3pm) User Contributed Perl Documentation Bio::TreeIO::NewickParser(3pm)NAME
Module which implements a newick string parser as a finite state machine which enables it to parse the full Newick specification.
Taken largely from the Ensembl Compara file with the same name (Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the parser
to work with BioPerl's event handler-based parsing scheme.
This module is used by nhx.pm and newick.pm, and is NOT called directly. Instead, both of those parsing modules extend this module in order
to gain access to the main parsing method.
SYNOPSIS
# From newick.pm
use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);
# in the next_tree method...
$self->parse_newick($_);
DESCRIPTION
This module correctly parses the Newick and NHX formats, sending calls to the BioPerl TreeEventHandler when appropriate in order to build
and populate the node objects.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
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