debian/README.Debian

 pscan-tfbs for Debian
 ---------------------
 
-Please note that on Debian systems we can not use the name pscan because
-there is another package with the very same name.  So the package is
-renamed to pscan-tfbs.
+Name conflict with pscan package
+================================
+
+We are facing a name clash in the Free Software universe and we have to
+circumvent this somehow.  In this package it is done was follows:
+
+  1. The pscan executable
+        /usr/lib/debian-med/bin/pscan
+
+  2. The executable in the default PATH is
+        /usr/bin/pscan-tfbs
+     (which is a symlink to the above executale)
+
+
+If you want to use pscan right from the command line just set the
+PATH variable like
+
+  export PATH=/usr/lib/debian-med/bin:$PATH
+
+If a user creates a file
+
+    ${HOME}/.blends
+
+with the content
+
+# Add Blend names here which should prepend its bin dir to PATH
+debian-med
+
+the med-config package automatically adds this PATH to the users
+environment (when using bash).
+
+
+JASPAR database
+===============
 
 Pscan depends on a transcription factor binding site description. The 
 database "JASPAR" can be downloaded with the Debian 'getData' interface.

debian/changelog

+pscan-tfbs (1.2.2-2) unstable; urgency=medium
+
+  * Team upload.
+  * Remove unused template files
+  * provide /usr/bin/pscan-tfbs to avoid file name conflict with pscan
+    package and keep the original upstream name in
+    /usr/lib/debian-med/bin/pscan
+    Closes: #901039
+  * Standards-Version: 4.1.4
+
+ -- Andreas Tille <tille@debian.org>  Fri, 08 Jun 2018 14:48:00 +0200
+
 pscan-tfbs (1.2.2-1) unstable; urgency=low
 
   [ Steffen Moeller ]

debian/control

@@ -5,7 +5,7 @@ Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
                libgsl-dev
-Standards-Version: 4.1.3
+Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/pscan-tfbs
 Vcs-Git: https://salsa.debian.org/med-team/pscan-tfbs.git
 Homepage: http://www.beaconlab.it/pscan

debian/manpages

-debian/pscan.1
+debian/*.1

debian/pscan-tfbs.install

-pscan	usr/bin
+pscan	usr/lib/debian-med/bin/

debian/pscan-tfbs.links

+usr/lib/debian-med/bin/pscan		usr/bin/pscan-tfbs
+# Also link the manpage to the Debian Med name space
+usr/share/man/man1/pscan-tfbs.1.gz	usr/lib/debian-med/share/man/man1/pscan.1.gz

debian/pscan.dirs

-usr/bin

debian/pscan.doc-base

-Document: pscan
-Title: Debian pscan Manual
-Author: G.Pesole,
- G.Pavesi <giulio.pavesi@unimi.it>,
- F.Zambelli <federico.zambelli@unimi.it>
-Abstract: The document resembles a UNIX man page.
-Section: science
-
-Format: text
-Files: /usr/share/doc/pscan/HELP.txt.gz

debian/pscan.install

-pscan /usr/bin