[med-svn] [freebayes] 03/03: Add patches for intial clean and cmake dependency

[Brad Chapman]

This is an automated email from the git hooks/post-receive script.

chapmanb-guest pushed a commit to branch master
in repository freebayes.

commit 0bfee0237c1ee96869c3443253b296b30bbd86ba
Author: chapmanb <chapmanb at 50mail.com>
Date:   Sun Feb 2 10:41:29 2014 -0500

    Add patches for intial clean and cmake dependency
---
 .gitignore                 |  9 ---------
 debian/changelog           |  2 +-
 debian/control             | 15 ++++++++-------
 debian/patches/clean.patch |  8 +++-----
 debian/rules               |  3 ---
 src/Makefile               |  2 +-
 6 files changed, 13 insertions(+), 26 deletions(-)

diff --git a/.gitignore b/.gitignore
index 7e817d2..e43b0f9 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,10 +1 @@
-test/
-bugs/
-*.bak
-*~
-.Rhistory
-simulation
-src/libbamtools.a
-performance
-math
 .DS_Store
diff --git a/debian/changelog b/debian/changelog
index 9c70b47..7471511 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
 freebayes (0.9.10.11-1) UNRELEASED; urgency=low
 
-  * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
+  * Initial FreeBayes packaging (Closes: #nnnn)
 
  -- Brad Chapman <chapmanb at 50mail.com>  Sun, 02 Feb 2014 05:14:33 -0500
diff --git a/debian/control b/debian/control
index f528923..734b026 100644
--- a/debian/control
+++ b/debian/control
@@ -2,7 +2,8 @@ Source: freebayes
 Section: science
 Priority: optional
 Maintainer: Brad Chapman <chapmanb at 50mail.com>
-Build-Depends: debhelper (>= 9)
+Build-Depends: debhelper (>= 9),
+               cmake (>= 2)
 Standards-Version: 3.9.5
 Homepage: https://github.com/ekg/freebayes
 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/freebayes.git
@@ -12,9 +13,9 @@ Package: freebayes
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: Bayesian haplotype-based polymorphism discovery and genotyping
-  FreeBayes is a Bayesian genetic variant detector designed to find
-  small polymorphisms, specifically SNPs (single-nucleotide
-  polymorphisms), indels (insertions and deletions), MNPs
-  (multi-nucleotide polymorphisms), and complex events (composite
-  insertion and substitution events) smaller than the length of a
-  short-read sequencing alignment.
\ No newline at end of file
+ FreeBayes is a Bayesian genetic variant detector designed to find
+ small polymorphisms, specifically SNPs (single-nucleotide
+ polymorphisms), indels (insertions and deletions), MNPs
+ (multi-nucleotide polymorphisms), and complex events (composite
+ insertion and substitution events) smaller than the length of a
+ short-read sequencing alignment.
\ No newline at end of file
diff --git a/debian/patches/clean.patch b/debian/patches/clean.patch
index e5d43c1..34aefeb 100644
--- a/debian/patches/clean.patch
+++ b/debian/patches/clean.patch
@@ -1,12 +1,10 @@
-Index: freebayes/src/Makefile
-===================================================================
---- freebayes.orig/src/Makefile	2014-02-02 06:40:47.242351987 -0500
-+++ freebayes/src/Makefile	2014-02-02 06:42:43.390356892 -0500
+--- freebayes.orig/src/Makefile
++++ freebayes/src/Makefile
 @@ -259,6 +259,6 @@
  
  clean:
  	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
 -	cd $(BAMTOOLS_ROOT)/build && make clean
-+	test -d $(BAMTOOLS_ROOT)/build && cd $(BAMTOOLS_ROOT)/build && make clean
++	test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean)
  	cd ../vcflib/smithwaterman && make clean
  
diff --git a/debian/rules b/debian/rules
index c30b66e..4067ba0 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,7 +1,4 @@
 #!/usr/bin/make -f
 
-# This has to be exported to make some magic below work.
-export DH_OPTIONS
-
 %:
 	dh $@ 
diff --git a/src/Makefile b/src/Makefile
index fc72a07..3fd822c 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -259,6 +259,6 @@ autoversion:
 
 clean:
 	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a}
-	cd $(BAMTOOLS_ROOT)/build && make clean
+	test ! -f $(BAMTOOLS_ROOT)/build/Makefile || (cd $(BAMTOOLS_ROOT)/build && make clean)
 	cd ../vcflib/smithwaterman && make clean
 

-- 
Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/freebayes.git