[med-svn] [wgs-assembler] 07/12: Remove packaging of kmer convenience copy and add dependency instead

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository wgs-assembler.

commit 422411b432238d49c4c5782d26e6ba762712eb8e
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Aug 8 00:10:31 2015 -0700

    Remove packaging of kmer convenience copy and add dependency instead
---
 debian/control                 | 29 +++--------------------------
 debian/libwgs-kmer-dev.install |  2 --
 debian/rules                   | 10 +++-------
 debian/wgs-kmer.install        |  1 -
 4 files changed, 6 insertions(+), 36 deletions(-)

diff --git a/debian/control b/debian/control
index 7c1b3b4..b308424 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,8 @@ Priority: optional
 Build-Depends: debhelper (>= 9),
                libbz2-dev,
                zlib1g-dev,
-               libbam-dev
+               libbam-dev,
+	       libmeryl-dev
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/wgs-assembler.git
 Vcs-Git: git://anonscm.debian.org/debian-med/wgs-assembler.git
@@ -18,6 +19,7 @@ Package: wgs-assembler
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
+	 meryl,
          tcsh
 Description: Whole-Genome DNA sequence assembler
  Celera Assembler is scientific software for DNA research. It can
@@ -47,28 +49,3 @@ Description: Whole-Genome DNA sequence assembler
  more difficult problems of biology.
  .
  See also: http://www.jcvi.org/cms/research/software/celera-assembler/overview/
-
-Package: wgs-kmer
-Architecture: any
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         wgs-assembler
-Provides: kmer
-Description: suite of tools for DNA sequence analysis
- The kmer package is a suite of tools for DNA sequence analysis. 
- It provides tools for searching (ESTs, mRNAs, sequencing reads); 
- aligning (ESTs, mRNAs, whole genomes); and a variety of analyses 
- based on kmers. 
-
-Package: libwgs-kmer-dev
-Architecture: any
-Section: libdevel
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-Description: suite of tools for DNA sequence analysis (development lib)
- The kmer package is a suite of tools for DNA sequence analysis. 
- It provides tools for searching (ESTs, mRNAs, sequencing reads); 
- aligning (ESTs, mRNAs, whole genomes); and a variety of analyses 
- based on kmers.
- .
- This package contains the static libraries and header files.
diff --git a/debian/libwgs-kmer-dev.install b/debian/libwgs-kmer-dev.install
deleted file mode 100644
index d627f2f..0000000
--- a/debian/libwgs-kmer-dev.install
+++ /dev/null
@@ -1,2 +0,0 @@
-kmer/installdir/lib		usr
-kmer/installdir/include/*	usr/include/kmer
diff --git a/debian/rules b/debian/rules
index b772a46..d89bf59 100755
--- a/debian/rules
+++ b/debian/rules
@@ -10,10 +10,9 @@ DEBPKGNAME     := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
 	dh $@ 
 
 override_dh_auto_build:
-	# do stuff for kmer
-	cd kmer && sh configure.sh && SAMTOOLS=/usr/include/samtools $(MAKE) install && ln -sf Linux-* installdir
-	# do stuff for wgs-assembler
-	$(MAKE) -C src
+	INC_SEARCH_PATH="/usr/include /usr/include/kmer" \
+	LIB_SEARCH_PATH="/usr/include /usr/include/kmer" \
+	  $(MAKE) -C src
 	ln -sf Linux-* installdir
 
 override_dh_install:
@@ -23,11 +22,8 @@ override_dh_install:
 	done
 
 override_dh_auto_clean:
-	cd kmer && $(MAKE) clean
 	$(MAKE) -C src clean
 	rm -rf Linux-* installdir
-	rm -rf kmer/Linux-* kmer/installdir kmer/Make.compilers
-	find kmer -name "*.d" -delete
 
 override_dh_fixperms:
 	dh_fixperms
diff --git a/debian/wgs-kmer.install b/debian/wgs-kmer.install
deleted file mode 100644
index f31c594..0000000
--- a/debian/wgs-kmer.install
+++ /dev/null
@@ -1 +0,0 @@
-kmer/installdir/bin		usr

-- 
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