[med-svn] r14449 - trunk/packages/cd-hit/trunk/debian

[Timothy Booth]

Author: tbooth-guest
Date: 2013-08-15 16:08:09 +0000 (Thu, 15 Aug 2013)
New Revision: 14449

Modified:
   trunk/packages/cd-hit/trunk/debian/changelog
   trunk/packages/cd-hit/trunk/debian/control
   trunk/packages/cd-hit/trunk/debian/links
   trunk/packages/cd-hit/trunk/debian/rules
Log:
A user was asking for cdhit-454, so I went to backport the latest version into
Bio-Linux, and added the link for this binary in the process.
Also, I couldn't see any need for OpenMPI (!= openmp), so removed the dep.


Modified: trunk/packages/cd-hit/trunk/debian/changelog
===================================================================
--- trunk/packages/cd-hit/trunk/debian/changelog	2013-08-15 15:45:50 UTC (rev 14448)
+++ trunk/packages/cd-hit/trunk/debian/changelog	2013-08-15 16:08:09 UTC (rev 14449)
@@ -1,3 +1,12 @@
+cd-hit (4.6.1-2012-08-27-1biolinux1) precise; urgency=low
+
+  * Rebuild for Precice
+  * Add new cdhit-454 to /usr/bin, including help2man manpage
+  * Remove dependency on openmpi, as cd-hit doesn't use it at all.
+    (It uses the -fopenmp compiler flag; maybe there was some confusion?)
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Thu, 15 Aug 2013 17:00:41 +0100
+
 cd-hit (4.6.1-2012-08-27-1) unstable; urgency=low
 
   * New upstream version (adapted patches)

Modified: trunk/packages/cd-hit/trunk/debian/control
===================================================================
--- trunk/packages/cd-hit/trunk/debian/control	2013-08-15 15:45:50 UTC (rev 14448)
+++ trunk/packages/cd-hit/trunk/debian/control	2013-08-15 16:08:09 UTC (rev 14449)
@@ -5,7 +5,6 @@
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               mpi-default-dev,
                help2man
 Standards-Version: 3.9.4
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cd-hit/trunk/
@@ -16,8 +15,7 @@
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${perl:Depends},
-         mpi-default-bin
+         ${perl:Depends}
 Description: suite of programs designed to quickly group sequences
  cd-hit contains a number of programs designed to quickly group
  sequences. cd-hit groups proteins into clusters that meet a user-defined

Modified: trunk/packages/cd-hit/trunk/debian/links
===================================================================
--- trunk/packages/cd-hit/trunk/debian/links	2013-08-15 15:45:50 UTC (rev 14448)
+++ trunk/packages/cd-hit/trunk/debian/links	2013-08-15 16:08:09 UTC (rev 14449)
@@ -1,6 +1,7 @@
 usr/lib/cd-hit/cd-hit			usr/bin/cdhit
 usr/lib/cd-hit/cd-hit-2d		usr/bin/cdhit-2d
 usr/lib/cd-hit/cd-hit-2d-para.pl	usr/bin/cd-hit-2d-para
+usr/lib/cd-hit/cd-hit-454		usr/bin/cdhit-454
 usr/lib/cd-hit/cd-hit-div.pl		usr/bin/cd-hit-div
 usr/lib/cd-hit/cd-hit-est		usr/bin/cdhit-est
 usr/lib/cd-hit/cd-hit-est-2d		usr/bin/cdhit-est-2d

Modified: trunk/packages/cd-hit/trunk/debian/rules
===================================================================
--- trunk/packages/cd-hit/trunk/debian/rules	2013-08-15 15:45:50 UTC (rev 14448)
+++ trunk/packages/cd-hit/trunk/debian/rules	2013-08-15 16:08:09 UTC (rev 14449)
@@ -28,6 +28,12 @@
 	   > $(mandir)/cdhit.1
 
 	help2man --no-info --no-discard-stderr --version-string='$(ver)' \
+	   --name='quickly group sequences, optimised for 454 data' \
+	   $(CURDIR)/cd-hit-454	| \
+	   sed -e 's/^cd-\(hit \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \
+	   > $(mandir)/cdhit-454.1
+
+	help2man --no-info --no-discard-stderr --version-string='$(ver)' \
 	   --name='quickly group sequences in db1 or db2 format' \
 	   $(CURDIR)/cd-hit-2d	| \
 	   sed -e 's/^cd-\(hit-2d \\-\)/cd\1/' -e 's/^.B cd-hit/.B cdhit/' \