Software / kPerl


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Contents          BLAST wrapper            wrapper to Staden's GAP4 package        more locale-specific utilities Staden's GAP4 package            internet-based utilities         phylogeny           generate plot diagrams using the GD package      basic sequence utilities: formatting, selection etc.       sequence motif analysis        statistics

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


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/ . This module works as an interface
     to external software.

Perl packages (CPAN) that are used throughout this suite. You will need to install these using cpan or cpanplus. 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 $FileHandle::Unget::VERSION 1.5, 1.6 [2004-09-12 SuSE 9.0] successfully used $FileHandle::Unget::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 now included in perl distribution, at least since 5.10.0 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 SeqAlign::AlnProj (function &AlnprojParamSprint). Usage of this module may be scattered even more in the future. MIME::Parser limited use in part of MIME-tools MIME::Parser depends on several other packages tried $MIME::Parser::VERSION 5.406, 2000-11-12 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 ) obsolete, former version of PWMscanNt (pwmsuite) RunPWMprot ) obsolete, former version of PWMscanAa (pwmsuite) 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: November 13, 2018.