BioPerl-Run

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lib/Bio/Tools/Run/Alignment/Amap.pm  view on Meta::CPAN

You will need to enable Amap to find the amap program. This can be
done in (at least) three ways:

  1. Make sure the amap executable is in your path (i.e. 
     'which amap' returns a valid program
  2. define an environmental variable AMAPDIR which points to a 
     directory containing the 'amap' app:
   In bash 
	export AMAPDIR=/home/progs/amap   or
   In csh/tcsh
        setenv AMAPDIR /home/progs/amap

  3. include a definition of an environmental variable AMAPDIR 
      in every script that will
     BEGIN {$ENV{AMAPDIR} = '/home/progs/amap'; }
     use Bio::Tools::Run::Alignment::Amap;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/Kalign.pm  view on Meta::CPAN

You will need to enable Kalign to find the kalign program. This can be
done in (at least) three ways:

  1. Make sure the kalign executable is in your path (i.e. 
     'which kalign' returns a valid program
  2. define an environmental variable KALIGNDIR which points to a 
     directory containing the 'kalign' app:
   In bash 
	export KALIGNDIR=/home/progs/kalign   or
   In csh/tcsh
        setenv KALIGNDIR /home/progs/kalign

  3. include a definition of an environmental variable KALIGNDIR 
      in every script that will
     BEGIN {$ENV{KALIGNDIR} = '/home/progs/kalign'; }
     use Bio::Tools::Run::Alignment::Kalign;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/MSAProbs.pm  view on Meta::CPAN

You will need to help MSAProbs to find the 'msaprobs' executable. This can 
be done in (at least) three ways:

  1. Make sure the msaprobs executable is in your path (i.e. 
     'which msaprobs' returns a valid program)
  2. define an environmental variable MSAPROBSDIR which points to a 
     directory containing the 'msaprobs' app:
   In bash 
	export MSAPROBSDIR=/home/progs/msaprobs   or
   In csh/tcsh
        setenv MSAPROBSDIR /home/progs/msaprobs

  3. include a definition of an environmental variable MSAPROBSDIR 
      in every script that will
     BEGIN {$ENV{MSAPROBSDIR} = '/home/progs/msaprobs'; }
     use Bio::Tools::Run::Alignment::MSAProbs;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/Muscle.pm  view on Meta::CPAN

You will need to enable Muscle to find the muscle program. This can be
done in (at least) three ways:

  1. Make sure the muscle executable is in your path (i.e.
     'which muscle' returns a valid program
  2. define an environmental variable MUSCLEDIR which points to a
     directory containing the 'muscle' app:
   In bash
    export MUSCLEDIR=/home/progs/muscle   or
   In csh/tcsh
        setenv MUSCLEDIR /home/progs/muscle

  3. include a definition of an environmental variable MUSCLEDIR
      in every script that will
     BEGIN {$ENV{MUSCLEDIR} = '/home/progs/muscle'; }
     use Bio::Tools::Run::Alignment::Muscle;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/Pal2Nal.pm  view on Meta::CPAN

 1. Make sure the script is in your path.
 2. Define an environmental variable PAL2NALDIR which is a 
    directory which contains the script:
    In bash:

    export PAL2NALDIR=/home/username/pal2nal/

    In csh/tcsh:

    setenv PAL2NALDIR /home/username/pal2nal

 3. Include a definition of an environmental variable PAL2NALDIR in
    every script that will use this Pal2Nal wrapper module, e.g.:

    BEGIN { $ENV{PAL2NALDIR} = '/home/username/pal2nal/' }
    use Bio::Tools::Run::Alignment::Pal2Nal;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/Probalign.pm  view on Meta::CPAN

You will need to enable Probalign to find the probalign program. This can be
done in (at least) three ways:

  1. Make sure the probalign executable is in your path (i.e. 
     'which probalign' returns a valid program
  2. define an environmental variable PROBALIGNDIR which points to a 
     directory containing the 'probalign' app:
   In bash 
	export PROBALIGNDIR=/home/progs/probalign   or
   In csh/tcsh
        setenv PROBALIGNDIR /home/progs/probalign

  3. include a definition of an environmental variable PROBALIGNDIR 
      in every script that will
     BEGIN {$ENV{PROBALIGNDIR} = '/home/progs/probalign'; }
     use Bio::Tools::Run::Alignment::Probalign;


=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/Probcons.pm  view on Meta::CPAN

You will need to enable Probcons to find the probcons program. This can be
done in (at least) three ways:

  1. Make sure the probcons executable is in your path (i.e. 
     'which probcons' returns a valid program
  2. define an environmental variable PROBCONSDIR which points to a 
     directory containing the 'probcons' app:
   In bash 
	export PROBCONSDIR=/home/progs/probcons   or
   In csh/tcsh
        setenv PROBCONSDIR /home/progs/probcons

  3. include a definition of an environmental variable PROBCONSDIR 
      in every script that will
     BEGIN {$ENV{PROBCONSDIR} = '/home/progs/probcons'; }
     use Bio::Tools::Run::Alignment::Probcons;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Alignment/Proda.pm  view on Meta::CPAN

You will need to enable Proda to find the proda program. This can be
done in (at least) three ways:

  1. Make sure the proda executable is in your path (i.e. 
     'which proda' returns a valid program
  2. define an environmental variable PRODADIR which points to a 
     directory containing the 'proda' app:
   In bash 
	export PRODADIR=/home/progs/proda   or
   In csh/tcsh
        setenv PRODADIR /home/progs/proda

  3. include a definition of an environmental variable PRODADIR 
      in every script that will
     BEGIN {$ENV{PRODADIR} = '/home/progs/proda'; }
     use Bio::Tools::Run::Alignment::Proda;


=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/FootPrinter.pm  view on Meta::CPAN

  http://www.mcb.mcgill.ca/~blanchem/FootPrinter2.1.tar.gz 


=head2 Running Footprinter

To run FootPrinter, you will need to set the environment variable
FOOTPRINTER_DIR to where the binary is located (even if the executable
is in your path). For example:

  setenv FOOTPRINTER_DIR /usr/local/bin/FootPrinter2.0/


=head2 Available Parameters

  PARAM         VALUES        DESCRIPTION
  ------------------------------------------------------------------------
  tree                      <file>     REQUIRED, Tree in Newick Format
                                       to evaluate parsimony score 
                                       REQUIRED unless tree_of_life
                                       exists in FOOTPRINTER_DIR

lib/Bio/Tools/Run/MCS.pm  view on Meta::CPAN

 1. Make sure the MCS scripts are in your path.
 2. Define an environmental variable MCSDIR which is a 
    directory which contains the MCS scripts:
    In bash:

    export MCSDIR=/home/username/mcs/

    In csh/tcsh:

    setenv MCSDIR /home/username/mcs

 3. Include a definition of an environmental variable MCSDIR in
    every script that will use this MCS wrapper module, e.g.:

    BEGIN { $ENV{MCSDIR} = '/home/username/mcs/' }
    use Bio::Tools::Run::MCS;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Match.pm  view on Meta::CPAN

 1. Make sure match is in your path.
 2. Define an environmental variable MATCHDIR which is a 
    directory which contains the match executable:
    In bash:

    export MATCHDIR=/home/username/match/

    In csh/tcsh:

    setenv MATCHDIR /home/username/match

 3. Include a definition of an environmental variable MATCHDIR in
    every script that will use this match wrapper module, e.g.:

    BEGIN { $ENV{MATCHDIR} = '/home/username/match/' }
    use Bio::Tools::Run::Match;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Gerp.pm  view on Meta::CPAN

 1. Make sure gerpcol and gerpelem are in your path.
 2. Define an environmental variable GERPDIR which is a 
    directory which contains the GERP executables:
    In bash:

    export GERPDIR=/home/username/gerp/

    In csh/tcsh:

    setenv GERPDIR /home/username/gerp

 3. Include a definition of an environmental variable GERPDIR in
    every script that will use this GERP wrapper module, e.g.:

    BEGIN { $ENV{GERPDIR} = '/home/username/gerp/' }
    use Bio::Tools::Run::Phylo::Gerp;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Njtree/Best.pm  view on Meta::CPAN

You will need to enable NJTREEDIR to find the njtree program. This can be
done in (at least) three ways:

  1. Make sure the njtree executable is in your path (i.e. 
     'which njtree' returns a valid program
  2. define an environmental variable NJTREEDIR which points to a 
     directory containing the 'njtree' app:
   In bash 
	export NJTREEDIR=/home/progs/treesoft/njtree   or
   In csh/tcsh
        setenv NJTREEDIR /home/progs/treesoft/njtree

  3. include a definition of an environmental variable NJTREEDIR 
      in every script that will
     BEGIN {$ENV{NJTREEDIR} = '/home/progs/treesoft/njtree'; }
     use Bio::Tools::Run::Phylo::Njtree::Best;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm  view on Meta::CPAN

 1. Make sure the phastCons and phyloFit executables are in your path.
 2. Define an environmental variable PHASTDIR which is a 
    directory which contains the phastCons and phyloFit applications:
    In bash:

    export PHASTDIR=/home/username/phast/bin

    In csh/tcsh:

    setenv PHASTDIR /home/username/phast/bin

 3. Include a definition of an environmental variable PHASTDIR in
    every script that will use this PhastCons wrapper module, e.g.:

    BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
    use Bio::Tools::Run::Phylo::Phast::PhastCons;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm  view on Meta::CPAN

 1. Make sure the phyloFit executable is in your path.
 2. Define an environmental variable PHASTDIR which is a 
    directory which contains the phyloFit application:
    In bash:

    export PHASTDIR=/home/username/phast/bin

    In csh/tcsh:

    setenv PHASTDIR /home/username/phast/bin

 3. Include a definition of an environmental variable PHASTDIR in
    every script that will use this PhyloFit wrapper module, e.g.:

    BEGIN { $ENV{PHASTDIR} = '/home/username/phast/bin' }
    use Bio::Tools::Run::Phylo::Phast::PhyloFit;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Phyml.pm  view on Meta::CPAN

=item 2.

Define an environmental variable PHYMLDIR which is a
directory which contains the 'phyml' application: In bash:

  export PHYMLDIR=/home/username/phyml_v2.4.4/exe

In csh/tcsh:

  setenv PHYMLDIR /home/username/phyml_v2.4.4/exe

=item 3.

Include a definition of an environmental variable PHYMLDIR in
every script that will use this Phyml wrapper module, e.g.:

  BEGIN { $ENV{PHYMLDIR} = '/home/username/phyml_v2.4.4/exe' }
  use Bio::Tools::Run::Phylo::Phyml;

=back

lib/Bio/Tools/Run/Phylo/QuickTree.pm  view on Meta::CPAN

 1. Make sure the QuickTree executable is in your path.
 2. Define an environmental variable QUICKTREEDIR which is a 
    directory which contains the 'quicktree' application:
    In bash:

    export QUICKTREEDIR=/home/username/quicktree_1.1/bin

    In csh/tcsh:

    setenv QUICKTREEDIR /home/username/quicktree_1.1/bin

 3. Include a definition of an environmental variable QUICKTREEDIR in
    every script that will use this QuickTree wrapper module, e.g.:

    BEGIN { $ENV{QUICKTREEDIR} = '/home/username/quicktree_1.1/bin' }
    use Bio::Tools::Run::Phylo::QuickTree;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Phylo/Semphy.pm  view on Meta::CPAN

 1. Make sure the Semphy executable is in your path.
 2. Define an environmental variable SEMPHYDIR which is a 
    directory which contains the Semphy application:
    In bash:

    export SEMPHYDIR=/home/username/semphy/

    In csh/tcsh:

    setenv SEMPHYDIR /home/username/semphy

 3. Include a definition of an environmental variable SEMPHYDIR in
    every script that will use this Semphy wrapper module, e.g.:

    BEGIN { $ENV{SEMPHYDIR} = '/home/username/semphy/' }
    use Bio::Tools::Run::Phylo::Semphy;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/RepeatMasker.pm  view on Meta::CPAN

 1. Make sure the RepeatMasker executable is in your path.
 2. Define an environmental variable REPEATMASKERDIR which is a
    directory which contains the RepeatMasker executable:
    In bash:

    export REPEATMASKERDIR=/home/username/RepeatMasker/

    In csh/tcsh:

    setenv REPEATMASKERDIR /home/username/RepeatMasker/

 3. Include a definition of an environmental variable REPEATMASKERDIR in
    every script that will use this RepeatMasker wrapper module, e.g.:

    BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
    use Bio::Tools::Run::RepeatMasker;

=head1 FEEDBACK

=head2 Mailing Lists

lib/Bio/Tools/Run/Simprot.pm  view on Meta::CPAN

You will need to enable SIMPROTDIR to find the simprot program. This can be
done in (at least) three ways:

  1. Make sure the simprot executable is in your path (i.e. 
     'which simprot' returns a valid program
  2. define an environmental variable SIMPROTDIR which points to a 
     directory containing the 'simprot' app:
   In bash 
	export SIMPROTDIR=/home/progs/simprot   or
   In csh/tcsh
        setenv SIMPROTDIR /home/progs/simprot

  3. include a definition of an environmental variable SIMPROTDIR 
      in every script that will
     BEGIN {$ENV{SIMPROTDIR} = '/home/progs/simprot'; }
     use Bio::Tools::Run::Simprot;

=head1 FEEDBACK

=head2 Mailing Lists