[med-svn] [manta] 01/02: Use Debian packaged htslib

[Andreas Tille]

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tille pushed a commit to branch master
in repository manta.

commit 228d9069bfe9f56e5a9866af4f71145a79030c58
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 15 16:51:30 2016 +0100

    Use Debian packaged htslib
---
 debian/control                                  |  3 +-
 debian/patches/series                           |  1 +
 debian/patches/use_debian_packaged_htslib.patch | 50 +++++++++++++++++++++++++
 3 files changed, 53 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index caf450f..60cf04f 100644
--- a/debian/control
+++ b/debian/control
@@ -15,7 +15,8 @@ Build-Depends: debhelper (>= 9),
                libboost-chrono-dev,
                libboost-test-dev,
                zlib1g-dev,
-               python-pyflow
+               python-pyflow,
+               libhts-dev
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/manta.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/manta.git
diff --git a/debian/patches/series b/debian/patches/series
index 3d28838..d96231c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 use_debian_packaged_pyflow.patch
 use_debian_packaged_zlib.patch
+use_debian_packaged_htslib.patch
diff --git a/debian/patches/use_debian_packaged_htslib.patch b/debian/patches/use_debian_packaged_htslib.patch
new file mode 100644
index 0000000..84e0de2
--- /dev/null
+++ b/debian/patches/use_debian_packaged_htslib.patch
@@ -0,0 +1,50 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 15 Nov 2016 14:29:08 +0100
+Description: Check for Debian packaged htslib
+
+--- a/redist/CMakeLists.txt
++++ b/redist/CMakeLists.txt
+@@ -58,42 +58,7 @@ endif()
+ #
+ # htslib
+ #
+-set(HTSLIB_PREFIX "htslib-1.2.1-204-g8197cfd")
+-superset(HTSLIB_DIR "${CMAKE_CURRENT_BINARY_DIR}/${HTSLIB_PREFIX}")
+-superset(HTSLIB_LIBRARY "${HTSLIB_DIR}/libhts.a")
+-
+-add_custom_command(
+-    OUTPUT ${HTSLIB_DIR}
+-    COMMAND ${CMAKE_COMMAND} -E remove_directory "${HTSLIB_DIR}"
+-    COMMAND ${CMAKE_COMMAND} -E tar xjf "${THIS_REDIST_DIR}/${HTSLIB_PREFIX}.tar.bz2"
+-    DEPENDS ${THIS_ZLIB}
+-    COMMENT "Unpacking htslib library")
+-
+-set (HTSLIB_FINAL_TASK ${HTSLIB_DIR})
+-
+-if (NOT WIN32)
+-    # note that htslib ./configure CFLAGS="custom" will overwrite the standard "-g -O2 -Wall" CFLAGS, so
+-    # we need to restore at least the -O2 for reasonable library performance:
+-    add_custom_command(
+-        OUTPUT ${HTSLIB_LIBRARY}
+-        COMMAND ./configure CC="${CMAKE_C_COMPILER}" CFLAGS='-O2 -I"${ZLIB_DIR}"' LIBS="${ZLIB_LIBRARY}" >htslib.config.log
+-        COMMAND $(MAKE) lib-static bgzip htsfile tabix >htslib.build.log 2>htslib.build.error.log
+-        WORKING_DIRECTORY ${HTSLIB_DIR}
+-        DEPENDS ${HTSLIB_DIR}
+-        COMMENT "Building htslib library")
+-
+-    set (HTSLIB_FINAL_TASK ${HTSLIB_LIBRARY})
+-endif ()
+-
+-set(THIS_HTSLIB "${THIS_PROJECT_NAME}_htslib")
+-add_custom_target(${THIS_HTSLIB} DEPENDS "${HTSLIB_FINAL_TASK}")
+-
+-
+-if (NOT WIN32)
+-    install(PROGRAMS "${HTSLIB_DIR}/bgzip" DESTINATION "${THIS_LIBEXECDIR}")
+-    install(PROGRAMS "${HTSLIB_DIR}/htsfile" DESTINATION "${THIS_LIBEXECDIR}")
+-    install(PROGRAMS "${HTSLIB_DIR}/tabix" DESTINATION "${THIS_LIBEXECDIR}")
+-endif ()
++superset(HTSLIB_LIBRARY "${CMAKE_INSTALL_LIBDIR}/libhts.a")
+ 
+ #
+ # samtools

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