[med-svn] r17535 - in trunk/packages/prodigal/trunk/debian: . patches source

[Olivier Sallou]

Author: osallou
Date: 2014-07-28 14:51:13 +0000 (Mon, 28 Jul 2014)
New Revision: 17535

Added:
   trunk/packages/prodigal/trunk/debian/patches/add_hardening
   trunk/packages/prodigal/trunk/debian/source/
   trunk/packages/prodigal/trunk/debian/source/format
Modified:
   trunk/packages/prodigal/trunk/debian/control
   trunk/packages/prodigal/trunk/debian/docs
   trunk/packages/prodigal/trunk/debian/patches/series
   trunk/packages/prodigal/trunk/debian/rules
Log:
generate man page from binary, add hardening flags to compilation

Modified: trunk/packages/prodigal/trunk/debian/control
===================================================================
--- trunk/packages/prodigal/trunk/debian/control	2014-07-28 14:32:13 UTC (rev 17534)
+++ trunk/packages/prodigal/trunk/debian/control	2014-07-28 14:51:13 UTC (rev 17535)
@@ -13,16 +13,33 @@
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: Microbial (bacterial and archaeal) gene finding program 
- Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal include:
+ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a
+ microbial (bacterial and archaeal) gene finding program developed at
+ Oak Ridge National Laboratory and the University of Tennessee.
+ Key features of Prodigal include:
  .
- Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
+ Speed: Prodigal is an extremely fast gene recognition tool
+ (written in very vanilla C). It can analyze an entire microbial genome
+ in 30 seconds or less.
  .
- Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
+ Accuracy: Prodigal is a highly accurate gene finder.
+ It correctly locates the 3' end of every gene in the experimentally verified
+ Ecogene data set (except those containing introns).
+ It possesses a very sophisticated ribosomal binding site scoring system that
+ enables it to locate the translation initiation site with great accuracy
+ (96% of the 5' ends in the Ecogene data set are located correctly).
  .
- Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
+ Specificity: Prodigal's false positive rate compares favorably with other
+ gene identification programs, and usually falls under 5%.
  .
- GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
+ GC-Content Indifferent: Prodigal performs well even in high GC genomes,
+ with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated
+ annotations.
  .
- Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
+ Metagenomic Version: Prodigal can run in metagenomic mode and analyze
+ sequences even when the organism is unknown.
  .
- Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
+ Ease of Use: Prodigal can be run in one step on a single genomic sequence
+ or on a draft genome containing many sequences. It does not need to be
+ supplied with any knowledge of the organism, as it learns all the properties
+ it needs to on its own.

Modified: trunk/packages/prodigal/trunk/debian/docs
===================================================================
--- trunk/packages/prodigal/trunk/debian/docs	2014-07-28 14:32:13 UTC (rev 17534)
+++ trunk/packages/prodigal/trunk/debian/docs	2014-07-28 14:51:13 UTC (rev 17535)
@@ -1,2 +1 @@
-CHANGES
 README

Added: trunk/packages/prodigal/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/prodigal/trunk/debian/patches/add_hardening	                        (rev 0)
+++ trunk/packages/prodigal/trunk/debian/patches/add_hardening	2014-07-28 14:51:13 UTC (rev 17535)
@@ -0,0 +1,20 @@
+Author: Olivier Sallou <osallou at debian.org>
+Subject: add Debian hardening
+Description: add compilation hardening flags
+Forwarded: no
+Last-Updated: 2014-07-28
+--- a/Makefile
++++ b/Makefile
+@@ -32,10 +32,10 @@
+ 
+ EXEC=	prodigal
+ 
+-CFLAGS=	-O3 -Wall
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) -O3 -Wall
+ 
+ LIBS=	-lm
+-LDFLAGS=	$(LIBS)
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) $(LIBS)
+ 
+ OBJS=	${SRC:.c=.o}
+ 

Modified: trunk/packages/prodigal/trunk/debian/patches/series
===================================================================
--- trunk/packages/prodigal/trunk/debian/patches/series	2014-07-28 14:32:13 UTC (rev 17534)
+++ trunk/packages/prodigal/trunk/debian/patches/series	2014-07-28 14:51:13 UTC (rev 17535)
@@ -1 +1,2 @@
 prevent_compilation_at_clean
+add_hardening

Modified: trunk/packages/prodigal/trunk/debian/rules
===================================================================
--- trunk/packages/prodigal/trunk/debian/rules	2014-07-28 14:32:13 UTC (rev 17534)
+++ trunk/packages/prodigal/trunk/debian/rules	2014-07-28 14:51:13 UTC (rev 17535)
@@ -3,5 +3,18 @@
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1
 
+CFLAGS=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+CFLAGS+=$(HARDENING_CFLAGS)
+LDFLAGS+=$(HARDENING_LDFLAGS)
+
 %:
 	dh $@
+
+override_dh_install:
+	help2man --no-discard-stderr ./prodigal  > prodigal.1
+	dh_install
+
+override_dh_clean:
+	dh_clean
+	rm -f prodigal.1

Added: trunk/packages/prodigal/trunk/debian/source/format
===================================================================
--- trunk/packages/prodigal/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/prodigal/trunk/debian/source/format	2014-07-28 14:51:13 UTC (rev 17535)
@@ -0,0 +1 @@
+3.0 (quilt)