Software / kPerl

 
 


Download kPerl kPerl-2.03.zip now;

Contents 

  Blast.pl          BLAST wrapper
  Gap.pl            wrapper to Staden's GAP4 package
  GscjGap.pl        more locale-specific utilities Staden's GAP4 package
  Net.pl            internet-based utilities
  Phylon.pl         phylogeny
  Plot.pl           generate plot diagrams using the GD package
  SeqHandle.pl      basic sequence utilities: formatting, selection etc.
  SeqMotif.pl       sequence motif analysis
  Statist.pl        statistics

  A detailed description for the frontend scripts of the package can be found
  in the package subdirectory DocExample/.

Installation 

To install the package and adjust it to your enviroment

(1) extract the package into an appropriate path, e.g.
     /usr/local/src .

(2) add the package path (e.g. /usr/local/src/kPerl) to
     the environment variable $PERL5LIB or define an extra
     environment variable $KPERLPATH .
     It may also be useful to add the package path to
     environment variable $PATH .

(3) install necessary CPAN modules that are listed in the
     package's file DocExample/ExternalDependencies.txt .

(4) adjusts path definitions in the package's module
     MainLib/Path.pm . This module works as an interface
     to external software.

Requirements 
Perl packages that are used throughout this suite, while they are not part of the Standard Library of the Perl distribution. CGI used in all CGI programs which are, however, not part of this suite, cmp. ~/prog/perl/RefCgi/ successfully used $CGI::VERSION 3.05 [2004-04-12 SuSE 9.0] successfully used $CGI::VERSION 3.08 [2005-04-25 SuSE 9.2] FileHandle::Unget essentially required by SeqLab::SeqStreamIn, preferably used by MainLib::Data, accounted for in SeqLab::SeqFormat WARNING: previous version 0.14 had a serious bug concerning method tell() which would cause fatals in SeqLab::SeqFormat. WARNING: versions 0.15, 0.16 (and previous?) won't install to certain environments, unless newest Scalar::Util is installed explicitly (CPAN won't recognise the dependency). And note that perl requires an API patch to support WeakRefs. successfully used $CGI::VERSION 1.5, 1.6 [2004-09-12 SuSE 9.0] successfully used $CGI::VERSION 1.621 [2005-04-25 SuSE 9.2] GD specific use of gdlib >= v1.20 (PNG support) The current package requires gdlib >= 2.0.12, including the header file. LWP::UserAgent limited use in Net.pl successfully used $LWP::UserAgent::VERSION 2.001 successfully used $LWP::UserAgent::VERSION 2.024 [2005-04-25 SuSE 9.2] Math::Round quite useful MemHandle currently used in SeqLab::SeqFormat (output filter "struct") and SeqLab::AlnProj (function &AlnprojParamSprint). Usage of this module may be scattered even more in the future. MIME::Parser limited use in Net.pl part of MIME-tools MIME::Parser depends on several other packages tried $MIME::Parser::VERSION 5.406, 2000-11-12 MIME::Base64 ? essentially required by AttMail.pl This will replace the dependency from binary program mmencode (see below). Binaries that are used in/wrapped through this suite and that are available from the author. LowCplx ... nblock fast processing of NNN joints in nucleotide sequences, esp. program function "-f split" PWMscanNt ... PWMscanProt ... RunPWMnt ... RunPWMprot ... Binaries that are used in / wrapped through this suite, while they are not part of the distribution. mmencode MIME coding/decoding part of the metamail program package it may be replaced by any other program or bunch of programs that allows coding/uncoding of MIME types -----------------------------------------------------------------------------
 


  Last update: April 05, 2017.