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

[Andreas Tille]

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tille pushed a commit to branch master
in repository manta.

commit bc6ed3a7212b7ee3f91541ec0880f9f7e643061c
Author: Andreas Tille <tille at debian.org>
Date:   Tue Nov 15 17:01:44 2016 +0100

    Use Debian packaged samtools
---
 debian/patches/series                             |  1 +
 debian/patches/use_debian_packaged_samtools.patch | 42 +++++++++++++++++++++++
 2 files changed, 43 insertions(+)

diff --git a/debian/patches/series b/debian/patches/series
index d96231c..4aa4fd1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 use_debian_packaged_pyflow.patch
 use_debian_packaged_zlib.patch
 use_debian_packaged_htslib.patch
+use_debian_packaged_samtools.patch
diff --git a/debian/patches/use_debian_packaged_samtools.patch b/debian/patches/use_debian_packaged_samtools.patch
new file mode 100644
index 0000000..5a1546d
--- /dev/null
+++ b/debian/patches/use_debian_packaged_samtools.patch
@@ -0,0 +1,42 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 15 Nov 2016 14:29:08 +0100
+Description: Check for Debian packaged samtools
+
+--- a/redist/CMakeLists.txt
++++ b/redist/CMakeLists.txt
+@@ -63,34 +63,11 @@ superset(HTSLIB_LIBRARY "${CMAKE_INSTALL
+ #
+ # samtools
+ #
+-set(SAMTOOLS_PREFIX "samtools-1.2")
+-set(SAMTOOLS_DIR "${CMAKE_CURRENT_BINARY_DIR}/${SAMTOOLS_PREFIX}")
+-set(SAMTOOLS_LIBRARY "${SAMTOOLS_DIR}/libbam.a")
++set(SAMTOOLS_DIR "/usr/bin")
+ superset(SAMTOOLS_PROG "${SAMTOOLS_DIR}/samtools")
+ 
+-# final directory copy below would ideally be a soft-link, copy is for windows build
+-add_custom_command(
+-    OUTPUT ${SAMTOOLS_DIR}
+-    COMMAND ${CMAKE_COMMAND} -E remove_directory "${SAMTOOLS_DIR}"
+-    COMMAND ${CMAKE_COMMAND} -E tar xjf "${THIS_REDIST_DIR}/${SAMTOOLS_PREFIX}.tar.bz2"
+-    COMMAND ${CMAKE_COMMAND} -E copy_directory "${HTSLIB_DIR}" "${SAMTOOLS_DIR}/${HTSLIB_PREFIX}"
+-    DEPENDS ${HTSLIB_FINAL_TASK}
+-    COMMENT "Unpacking samtools package")
+-
+ set (SAMTOOLS_FINAL_TASK ${SAMTOOLS_DIR})
+ 
+-if (NOT WIN32)
+-    add_custom_command(
+-        OUTPUT ${SAMTOOLS_PROG}
+-        COMMAND $(MAKE) HTSDIR=${HTSLIB_PREFIX} all 2>| samtools.build.log
+-        DEPENDS ${HTSLIB_LIBRARY}
+-        DEPENDS ${SAMTOOLS_DIR}
+-        WORKING_DIRECTORY ${SAMTOOLS_DIR}
+-        COMMENT "Building samtools package")
+-
+-    set (SAMTOOLS_FINAL_TASK ${SAMTOOLS_PROG})
+-endif ()
+-
+ set(THIS_SAMTOOLS "${THIS_PROJECT_NAME}_samtools")
+ add_custom_target(${THIS_SAMTOOLS} DEPENDS "${SAMTOOLS_FINAL_TASK}")
+ 

-- 
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