[med-svn] r19859 - in trunk/packages/sumatra/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-08-06 13:30:48 +0000 (Thu, 06 Aug 2015)
New Revision: 19859

Added:
   trunk/packages/sumatra/trunk/debian/doc-base
   trunk/packages/sumatra/trunk/debian/patches/no_zlib.patch
Removed:
   trunk/packages/sumatra/trunk/debian/patches/no_zlib
Modified:
   trunk/packages/sumatra/trunk/debian/patches/series
   trunk/packages/sumatra/trunk/debian/rules
Log:
Polishing packaging


Added: trunk/packages/sumatra/trunk/debian/doc-base
===================================================================
--- trunk/packages/sumatra/trunk/debian/doc-base	                        (rev 0)
+++ trunk/packages/sumatra/trunk/debian/doc-base	2015-08-06 13:30:48 UTC (rev 19859)
@@ -0,0 +1,16 @@
+Document: sumatra
+Title: Sumatra: fast and exact comparison of sequences
+Author: Céline Mercier <celine.mercier at metabarcoding.org>
+Abstract: With the development of next-generation sequencing, efficient tools are needed to handle millions of
+ sequences in reasonable amounts of time. Sumatra is a program developed by the LECA. Sumatra aims to
+ compare sequences in a way that is fast and exact at the same time. This tool has been developed to be
+ adapted to the type of data generated by DNA metabarcoding, i.e. entirely sequenced, short markers.
+ Sumatra computes the pairwise alignment scores from one dataset or between two datasets, with the
+ possibility to specify a similarity threshold under which pairs of sequences that have a lower similarity are
+ not reported. The output can then go through a classification process with programs such as MCL or
+ MOTHUR. Currently, Sumatra is available as a program that you can download and install on Unix-like
+ machines.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/sumatra/sumatra_user_manual.pdf

Deleted: trunk/packages/sumatra/trunk/debian/patches/no_zlib
===================================================================
--- trunk/packages/sumatra/trunk/debian/patches/no_zlib	2015-08-06 12:54:39 UTC (rev 19858)
+++ trunk/packages/sumatra/trunk/debian/patches/no_zlib	2015-08-06 13:30:48 UTC (rev 19859)
@@ -1,12 +0,0 @@
-There is no actual use of Zlib, so no need to build against it.
---- a/sumatra/Makefile
-+++ b/sumatra/Makefile
-@@ -8,7 +8,7 @@
- 
- SRCS= $(SUMATRA_SRC)
- 
--LIB= -lfasta -llcs -lfile -lutils -lz -lm
-+LIB= -lfasta -llcs -lfile -lutils -lm
- 
- LIBFASTA = ../libfasta/libfasta.a
- LIBLCS   = ../liblcs/liblcs.a

Copied: trunk/packages/sumatra/trunk/debian/patches/no_zlib.patch (from rev 19845, trunk/packages/sumatra/trunk/debian/patches/no_zlib)
===================================================================
--- trunk/packages/sumatra/trunk/debian/patches/no_zlib.patch	                        (rev 0)
+++ trunk/packages/sumatra/trunk/debian/patches/no_zlib.patch	2015-08-06 13:30:48 UTC (rev 19859)
@@ -0,0 +1,15 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Fri, 13 Feb 2015 16:24:17 +0000
+Description There is no actual use of Zlib, so no need to build against it.
+
+--- a/Makefile
++++ b/Makefile
+@@ -8,7 +8,7 @@ SUMATRA_OBJ= $(patsubst %.c,%.o,$(SUMATR
+ 
+ SRCS= $(SUMATRA_SRC)
+ 
+-LIB= -lfasta -llcs -lfile -lutils -lz -lm
++LIB= -lfasta -llcs -lfile -lutils -lm
+ 
+ include ./global.mk
+ 

Modified: trunk/packages/sumatra/trunk/debian/patches/series
===================================================================
--- trunk/packages/sumatra/trunk/debian/patches/series	2015-08-06 12:54:39 UTC (rev 19858)
+++ trunk/packages/sumatra/trunk/debian/patches/series	2015-08-06 13:30:48 UTC (rev 19859)
@@ -1 +1,2 @@
 hardening.patch
+no_zlib.patch

Modified: trunk/packages/sumatra/trunk/debian/rules
===================================================================
--- trunk/packages/sumatra/trunk/debian/rules	2015-08-06 12:54:39 UTC (rev 19858)
+++ trunk/packages/sumatra/trunk/debian/rules	2015-08-06 13:30:48 UTC (rev 19859)
@@ -12,3 +12,12 @@
 	#Upstream is very messy.  Scrub out all the .svn stuff
 	#and .o files.
 	find sumalibs -name '*.[oa]' -delete
+
+override_dh_compress:
+	dh_compress --exclude=.pdf
+
+# May be it makes sense at some point in time to use *.md
+# source for the manpage - currently the result is not really
+# the usual manpage structure
+#override_dh_installman:
+#	go-md2man -in=sumatra_user_manual.md -out=sumatra.1
\ No newline at end of file