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 to Debian,
e.g. r-cran-qtl and general packages for bioinformatics research.


Name conflict with plink1, plink1.9, plink2 and plink from ssh clone putty
=============================================

At http://bugs.debian.org/503367 and http://bugs.debian.org/771154#25
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.  To summarize, we have:

  1. The plink1 executable
        /usr/lib/debian-med/bin/plink
  1.1 A symbolic link to the plink1 executable
             /usr/bin/plink1
             /usr/bin/p-link
             /usr/lib/plink/plink

  2. The plink1.9 executable
        /usr/lib/debian-med/bin/plink1.9
  2.1 A symbolic link to the plink1.9 executable
             /usr/bin/plink1.9

  3. The plink2 executable
        /usr/lib/debian-med/bin/plink2
  3.1 A symbolic link to the plink2 executable
             /usr/bin/plink2

  4. The plink executable (from putty)
        /usr/bin/plink

So if you want to use plink1 with its original name just do the
following:  Set the PATH variable like

  export PATH=/usr/lib/debian-med/bin:$PATH

This makes sure that scripts you are using will find the correct plink executable.

 -- Dylan Aïssi <bob.dybian@gmail.com>  Thu, 22 Jan 2015 08:00:59 +0100
