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plink - whole-genome association analysis toolset…  more info»

README.Debian

plink for Debian
----------------

plink is a very fine piece of software and the world should thank
the authors for their efforts. plink knows how to interact
with gplink and haploview. The packaging of the latter is already
being prepared. The prior still seeks a maintainer.

Users of plink may also be interested in other packages the that
Debian-Med.alioth.debian.org community has brought ot Debian,
e.g. r-cran-qtl and general packages for bioinformatics research.


Name conflict with plink from ssh clone putty
=============================================

At http://bugs.debian.org/503367 you can read the full discussion
about a name clash between one component of the frequently used
ssh software putty and plink.  The short story is: We are facing a
name clash in the Free Software universe and we have to circumvent
this somehow.  Following the arguing in the bug discussion the
plink package has to do the name change.  So we found the following
solution:

  1. The plink executable will be copied to
        /usr/lib/plink/plink
  2. A symlink
        /usr/bin/p-link
     points to this location.

So if you want to use plink with its original name just do the
following:  Set the PATH variable like

  export PATH="/usr/lib/plink:$PATH"

or alternatively set a symlink into a directory which is normally in
your PATH anyway like

  ln -s /usr/lib/plink/plink /usr/local/bin/plink

if /usr/local/bin is in your PATH.  This makes sure that scripts you
are using will find the correct plink executable.

 -- Andreas Tille <tille@debian.org>  Tue, 31 Mar 2009 22:28:25 +0200
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