[med-svn] [lambda-align] 12/15: work on initial packaging

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository lambda-align.

commit 70d641fd245694aa85c8f8d22820f9ee74fcce08
Author: Sascha Steinbiss <satta at debian.org>
Date:   Fri Aug 19 15:28:00 2016 +0000

    work on initial packaging
---
 debian/changelog                         |  2 +-
 debian/control                           |  4 ++--
 debian/patches/cmake-seqan-modules.patch | 11 +++++++++++
 debian/patches/gcc-6.patch               | 11 +++++++++++
 debian/patches/series                    |  2 ++
 debian/rules                             |  8 +++-----
 6 files changed, 30 insertions(+), 8 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 8240e89..5fddf0d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-lambda-align (1.9.0-1) unstable; urgency=medium
+lambda-align (1.0.0-1) unstable; urgency=medium
 
   * Initial release (Closes: #<bug>)
 
diff --git a/debian/control b/debian/control
index 3971d4b..6804ff5 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,7 @@ Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
 Build-Depends: debhelper (>= 9),
-               seqan-dev,
+               libseqan2-dev,
                cmake,
                zlib1g-dev,
                libbz2-dev
@@ -21,4 +21,4 @@ Description: Local Aligner for Massive Biological DatA
  and searches in protein space. It is compatible to the de facto standard tool
  BLAST, but often outperforms the best currently available alternatives at
  reproducing BLAST’s results and is the fastest compared with the current
- state of the art at comparable levels of sensitivity.
\ No newline at end of file
+ state of the art at comparable levels of sensitivity.
diff --git a/debian/patches/cmake-seqan-modules.patch b/debian/patches/cmake-seqan-modules.patch
new file mode 100644
index 0000000..602b4b3
--- /dev/null
+++ b/debian/patches/cmake-seqan-modules.patch
@@ -0,0 +1,11 @@
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -22,6 +22,8 @@
+ # Dependencies (continued)
+ # ----------------------------------------------------------------------------
+ 
++LIST(APPEND CMAKE_MODULE_PATH "/usr/share/seqan/cmake")
++
+ # Search SeqAn and select dependencies.
+ find_package(OpenMP QUIET)
+ find_package(ZLIB   QUIET)
diff --git a/debian/patches/gcc-6.patch b/debian/patches/gcc-6.patch
new file mode 100644
index 0000000..27d693a
--- /dev/null
+++ b/debian/patches/gcc-6.patch
@@ -0,0 +1,11 @@
+--- a/src/lambda.hpp
++++ b/src/lambda.hpp
+@@ -1960,7 +1960,7 @@
+     typedef typename Size<typename TLocalHolder::TAlignRow0>::Type      TSize;
+     typedef TraceSegment_<TPos, TSize>                                  TTraceSegment;
+ 
+-    typedef typename SimdVector<int16_t>::Type                          TSimdAlign;
++    typedef SimdVector<int16_t>::Type                          TSimdAlign;
+ 
+     unsigned const numAlignments = length(lH.matches);
+     unsigned const sizeBatch = LENGTH<TSimdAlign>::VALUE;
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..036506e
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+cmake-seqan-modules.patch
+gcc-6.patch
diff --git a/debian/rules b/debian/rules
index bb2dee8..95a7897 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,11 +1,9 @@
 #!/usr/bin/make -f
 
-DEBVERS        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-VERSION        := $(shell echo '$(DEBVERS)' | egrep -o '[0-9]+\.[0-9]+\.[0-9]+')
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
 	dh $@
 
-override_dh_auto_build:
-	mkdir build
-	cd build && cmake .. -DLAMBDA_NATIVE_BUILD=0 && make
\ No newline at end of file
+override_dh_auto_configure:
+	dh_auto_configure -- -DLAMBDA_NATIVE_BUILD=OFF -DLAMBDA_MMAPPED_DB=ON

-- 
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