[med-svn] [salmon] 01/01: Try to use debian packaged rapmap

[Andreas Tille]

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

tille pushed a commit to branch master
in repository salmon.

commit 796596c58c655b379313651c34a9cb29681e00c5
Author: Andreas Tille <tille at debian.org>
Date:   Wed Sep 7 12:43:18 2016 +0200

    Try to use debian packaged rapmap
---
 debian/control                                  |  3 +-
 debian/patches/series                           |  1 +
 debian/patches/use_debian_packaged_rapmap.patch | 75 +++++++++++++++++++++++++
 3 files changed, 78 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 64fa39e..b178a96 100644
--- a/debian/control
+++ b/debian/control
@@ -23,7 +23,8 @@ Build-Depends: debhelper (>= 9),
                sphinx-doc,
                python-sphinx | python3-sphinx,
                zlib1g-dev,
-               libeigen3-dev
+               libeigen3-dev,
+               rapmap
 Standards-Version: 3.9.7
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/salmon.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/salmon.git
diff --git a/debian/patches/series b/debian/patches/series
index fb2afc8..f665fe7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ use-system-pkg-config-tbb
 0007-Remove-unnecessarily-linked-libraries.patch
 0008-Remove-salmon_core-lib.patch
 0009-Remove-FIND_PACKAGE-for-liblzma-and-libbz2.patch
+use_debian_packaged_rapmap.patch
diff --git a/debian/patches/use_debian_packaged_rapmap.patch b/debian/patches/use_debian_packaged_rapmap.patch
new file mode 100644
index 0000000..1fc2b2d
--- /dev/null
+++ b/debian/patches/use_debian_packaged_rapmap.patch
@@ -0,0 +1,75 @@
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -5,7 +5,6 @@ ${GAT_SOURCE_DIR}/include
+ ${ZLIB_INCLUDE_DIR}
+ ${TBB_INCLUDE_DIRS}
+ ${Boost_INCLUDE_DIRS}
+-${GAT_SOURCE_DIR}/external/install/include/rapmap
+ )
+ 
+ if (JELLYFISH_FOUND)
+@@ -20,14 +19,6 @@ is.c
+ bwt_gen.c
+ bwtindex.c
+ xxhash.c
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapFileSystem.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAIndexer.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAIndex.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapSAMapper.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/RapMapUtils.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/HitManager.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/rank9b.cpp
+-${GAT_SOURCE_DIR}/external/install/src/rapmap/bit_array.c
+ CollapsedEMOptimizer.cpp
+ CollapsedGibbsSampler.cpp
+ Salmon.cpp
+@@ -39,7 +30,6 @@ SequenceBiasModel.cpp
+ StadenUtils.cpp
+ TranscriptGroup.cpp
+ GZipWriter.cpp
+-#${GAT_SOURCE_DIR}/external/install/src/rapmap/sais.c
+ )
+ 
+ set (SALMON_ALIGN_SRCS
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -161,7 +161,7 @@ set (CMAKE_VERBOSE_MAKEFILE true)
+ #
+ ####
+ if(NOT FETCHED_RAPMAP)
+-  exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
++  # exec_program(${CMAKE_CURRENT_SOURCE_DIR}/scripts/fetchRapMap.sh)
+   set(FETCHED_RAPMAP TRUE CACHE BOOL "Has RapMap been fetched?" FORCE)
+ endif()
+ 
+@@ -584,18 +584,18 @@ endif()
+ ##
+ ## This depenency is for RapMap
+ ##
+-message("Build system will fetch and build SparseHash")
+-message("==================================================================")
+-ExternalProject_Add(libsparsehash
+-    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
+-    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
+-        tar -xzf sparsehash-2.0.2.tar.gz
+-    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
+-    BUILD_IN_SOURCE TRUE
+-    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
+-    CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
+-    INSTALL_COMMAND make install
+-)
++#message("Build system will fetch and build SparseHash")
++#message("==================================================================")
++#ExternalProject_Add(libsparsehash
++#    DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external
++#    DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/sparsehash/archive/sparsehash-2.0.2.tar.gz -o sparsehash-2.0.2.tar.gz &&
++#        tar -xzf sparsehash-2.0.2.tar.gz
++#    SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/sparsehash-sparsehash-2.0.2
++#    BUILD_IN_SOURCE TRUE
++#    INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install
++#    CONFIGURE_COMMAND sh -c "CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ./configure --prefix=<INSTALL_DIR>"
++#    INSTALL_COMMAND make install
++#)
+ 
+ ###
+ #

-- 
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