[med-svn] [rapmap] 03/03: Prepared for new version 0.5

Steffen Möller moeller at moszumanska.debian.org
Sun Oct 22 19:28:23 UTC 2017 

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

moeller pushed a commit to branch master
in repository rapmap.

commit c4b732bcb0c984707eb3f6363566fc495ceaf4e1
Author: Steffen Moeller <moeller at debian.org>
Date:   Sun Oct 22 21:23:12 2017 +0200

    Prepared for new version 0.5
---
 debian/changelog                     | 12 +++++++++
 debian/control                       |  2 +-
 debian/patches/use-debian-libs.patch | 48 +++++++++++++++++++-----------------
 debian/rules                         |  5 ++++
 4 files changed, 44 insertions(+), 23 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index ed7fa0d..3a308ed 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,15 @@
+rapmap (0.5.0+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+
+  * New upstream version.
+  * Added references to registries.
+  * Bumped policy to 4.1.1.1 (no changes required).
+
+  * Removing files created during build in debian/rules clean target
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 22 Oct 2017 21:19:17 +0200
+
 rapmap (0.4.0+dfsg-2) unstable; urgency=medium
 
   * Set NO_NATIVE_ARCH=true
diff --git a/debian/control b/debian/control
index 4bdd2e3..0d25286 100644
--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 10),
                libtclap-dev,
                pkg-config,
                python-markdown
-Standards-Version: 3.9.8
+Standards-Version: 4.1.1.1
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/rapmap.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/rapmap.git
 Homepage: https://github.com/COMBINE-lab/RapMap
diff --git a/debian/patches/use-debian-libs.patch b/debian/patches/use-debian-libs.patch
index 28c8643..291a76e 100644
--- a/debian/patches/use-debian-libs.patch
+++ b/debian/patches/use-debian-libs.patch
@@ -2,9 +2,11 @@ Description: make RapMap use Debian's versions of dependencies
  This involves disabling downloads and adjusting API usage to the versions
  packaged in Debian.
 Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -165,20 +165,6 @@ if (NOT ZLIB_FOUND)
+Index: rapmap/CMakeLists.txt
+===================================================================
+--- rapmap.orig/CMakeLists.txt
++++ rapmap/CMakeLists.txt
+@@ -168,20 +168,6 @@ if (NOT ZLIB_FOUND)
  endif()
  
  
@@ -25,33 +27,33 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  if (NOT CEREAL_ROOT)
  	set(CEREAL_ROOT ${GAT_SOURCE_DIR}/external/install)
  endif()
-@@ -211,24 +197,7 @@ if (NOT JELLYFISH_ROOT)
+@@ -214,25 +200,6 @@ if (NOT JELLYFISH_ROOT)
  	set(JELLYFISH_ROOT ${GAT_SOURCE_DIR}/external/install)
  endif()
  
--find_package(Jellyfish 2.2.5)
+-find_package(Jellyfish 2.2.6)
 -
 -if (NOT JELLYFISH_FOUND)
 -message("Build system will fetch and build Jellyfish")
 -message("==================================================================")
 -ExternalProject_Add(libjellyfish
 -    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--    DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.5/jellyfish-2.2.5.tar.gz -o jellyfish-2.2.5.tgz &&
--    	rm -fr jellyfish-2.2.5 &&
--     	tar -xzvf jellyfish-2.2.5.tgz
--    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz -o jellyfish-2.2.6.tgz &&
+-    	rm -fr jellyfish-2.2.6 &&
+-     	tar -xzvf jellyfish-2.2.6.tgz
+-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6
 -    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.5/configure --enable-shared=no --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
--    BUILD_COMMAND ${MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
+-    CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/jellyfish-2.2.6/configure --enable-shared=no --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
+-    BUILD_COMMAND make CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CXXFLAGS=${JELLYFISH_CXX_FLAGS}
 -    BUILD_IN_SOURCE 1
 -    INSTALL_COMMAND make install
 -)
 -endif()
-+#find_package(Jellyfish 2.2.5)
- 
+-
  set (FAST_MALLOC_LIB "")
  set (HAVE_FAST_MALLOC FALSE)
-@@ -252,24 +221,6 @@ if (NOT HAVE_FAST_MALLOC)
+ 
+@@ -255,24 +222,6 @@ if (NOT HAVE_FAST_MALLOC)
      endif()
  endif()
  
@@ -60,12 +62,12 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
 -    message("==================================================================")
 -    ExternalProject_Add(libjemalloc
 -        DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
--        DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/3.6.0.tar.gz -o jemalloc-3.6.0.tar.gz &&
--        tar -xzf jemalloc-3.6.0.tar.gz
--        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-3.6.0
+-        DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/jemalloc/archive/4.5.0.tar.gz -o jemalloc-4.5.0.tar.gz &&
+-                         tar -xzf jemalloc-4.5.0.tar.gz
+-        SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/jemalloc-4.5.0
 -        BUILD_IN_SOURCE TRUE
 -        INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
--        CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} ./autogen.sh --prefix=<INSTALL_DIR>"
+-        CONFIGURE_COMMAND sh -c "${JEMALLOC_FLAGS} ./autogen.sh --disable-debug --prefix=<INSTALL_DIR>"
 -        INSTALL_COMMAND cp -r lib <INSTALL_DIR>/ && cp -r include <INSTALL_DIR>/
 -        )
 -
@@ -76,11 +78,13 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
  ###
  #
  # Done building external dependencies.
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
+Index: rapmap/src/CMakeLists.txt
+===================================================================
+--- rapmap.orig/src/CMakeLists.txt
++++ rapmap/src/CMakeLists.txt
 @@ -84,9 +84,12 @@ set (SUFFARRAY64_LIB ${GAT_SOURCE_DIR}/e
  target_link_libraries(rapmap
-     ${PTHREAD_LIB}
+     # ${PTHREAD_LIB}
      ${ZLIB_LIBRARY}
 -    ${SUFFARRAY_LIB}
 -    ${SUFFARRAY64_LIB}
@@ -92,5 +96,5 @@ Author: Sascha Steinbiss <sascha at steinbiss.name>
 +    divsufsort64
 +    jellyfish-2.0
      m
-     ${LIBLZMA_LIBRARIES}
+     #${LIBLZMA_LIBRARIES}
      ${NON_APPLECLANG_LIBS}
diff --git a/debian/rules b/debian/rules
index c438c77..aabbc39 100755
--- a/debian/rules
+++ b/debian/rules
@@ -14,3 +14,8 @@ override_dh_auto_configure:
 override_dh_auto_build:
 	dh_auto_build
 	markdown_py -f README.html README.md
+
+override_dh_clean:
+	dh_clean README.html sample_data/sample_quasi_index/ sample_data/sample_quasi_index_ph/ sample_data/sample_quasi_map.sam sample_data/sample_quasi_map_ph.sam
+
+	

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