[med-svn] [salmon] 01/05: more CMake tweaks

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository salmon.

commit 64f382afcc602ec0f0702f523c48921485250eeb
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Sat Jan 30 05:43:34 2016 -0800

    more CMake tweaks
---
 debian/copyright                |  2 ++
 debian/patches/cmake-typo-fixes | 10 ++++++++--
 debian/patches/dependency-fix   | 18 ++++++++++++------
 debian/patches/series           |  1 +
 4 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index f8f41e8..d73ccaf 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -4,6 +4,8 @@ Source: https://github.com/COMBINE-lab/salmon/
 Files-Excluded: doc/build/*
  include/CollapsedIterativeOptimizer.hpp.bak
  src/SalmonQuantify.cpp.bak
+ include/eigen3
+ include/obsolete
 
 Files: *
 Copyright: © 2015 The Salmon Authors
diff --git a/debian/patches/cmake-typo-fixes b/debian/patches/cmake-typo-fixes
index 67c9795..fbdd368 100644
--- a/debian/patches/cmake-typo-fixes
+++ b/debian/patches/cmake-typo-fixes
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <crusoe at ucdavis.edu>
 Description: fix upstream's typos
 --- salmon.orig/CMakeLists.txt
 +++ salmon/CMakeLists.txt
-@@ -6,8 +6,8 @@
+@@ -6,12 +6,12 @@
  
  set(CPACK_PACKAGE_VERSION "0.4.2")
  set(CPACK_PACKAGE_VERSION_MAJOR "0")
@@ -12,7 +12,13 @@ Description: fix upstream's typos
 +set(CPACK_PACKAGE_VERSION_PATCH "2")
  set(CPACK_GENERATOR "TGZ")
  set(CPACK_SOURCE_GENERATOR "TGZ")
- set(CPACK_PACKAGE_VENDOR Stony Brook University")
+-set(CPACK_PACKAGE_VENDOR Stony Brook University")
+-set(CPACK_PACKAGE_DESCRIPTION_SUMMARY Salmon - Wicked-fast RNA-seq isoform quantification using lightweight alignments")
++set(CPACK_PACKAGE_VENDOR "Stony Brook University")
++set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Salmon - Wicked-fast RNA-seq isoform quantification using lightweight alignments")
+ set(CPACK_PACKAGE_NAME 
+   "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+ set(CPACK_SOURCE_PACKAGE_FILE_NAME
 --- salmon.orig/include/tensemble/GBMRegressor.h
 +++ salmon/include/tensemble/GBMRegressor.h
 @@ -63,7 +63,7 @@
diff --git a/debian/patches/dependency-fix b/debian/patches/dependency-fix
index 6f061df..757a267 100644
--- a/debian/patches/dependency-fix
+++ b/debian/patches/dependency-fix
@@ -384,16 +384,22 @@ Description: Use Debian version of dependencies, don't download them
  #
 --- salmon.orig/src/CMakeLists.txt
 +++ salmon/src/CMakeLists.txt
-@@ -43,7 +43,7 @@
- ${GAT_SOURCE_DIR}/external/cereal/include
- ${GAT_SOURCE_DIR}/external/install/include
- ${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.1.3
+@@ -38,12 +38,8 @@
+ 
+ include_directories( 
+ ${GAT_SOURCE_DIR}/include
+-${GAT_SOURCE_DIR}/include/eigen3
+-${GAT_SOURCE_DIR}/external
+-${GAT_SOURCE_DIR}/external/cereal/include
+-${GAT_SOURCE_DIR}/external/install/include
+-${GAT_SOURCE_DIR}/external/install/include/jellyfish-2.1.3
 -${GAT_SOURCE_DIR}/external/install/include/bwa
++/usr/include/eigen3
 +/usr/include/bwa
  ${ZLIB_INCLUDE_DIR}
  ${TBB_INCLUDE_DIRS}
  ${Boost_INCLUDE_DIRS}
-@@ -74,7 +74,7 @@
+@@ -74,7 +70,7 @@
  set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
  
  # Build the Salmon library
@@ -402,7 +408,7 @@ Description: Use Debian version of dependencies, don't download them
  
  # Build the salmon executable
  add_executable(salmon ${SALMON_MAIN_SRCS} ${SALMON_ALIGN_SRCS})
-@@ -107,10 +107,10 @@
+@@ -107,10 +103,10 @@
      gff
      ${PTHREAD_LIB}
      ${Boost_LIBRARIES} 
diff --git a/debian/patches/series b/debian/patches/series
index bf7d00f..e08a900 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -4,3 +4,4 @@ cmake-adj
 drop-mathjax
 cmake-typo-fixes
 disable-version-check
+system-eigen3

-- 
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