[med-svn] [sra-sdk] 01/01: proper hdf5 linking, hdf5 also seems to need libsz (https://github.com/PacificBiosciences/blasr/issues/4)

[Andreas Tille]

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tille pushed a commit to branch master
in repository sra-sdk.

commit 62dbed5c5a603e4aa562553df7c3196fda21fde2
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 22 22:48:17 2016 +0200

    proper hdf5 linking, hdf5 also seems to need libsz (https://github.com/PacificBiosciences/blasr/issues/4)
---
 debian/control                                 |  1 +
 debian/patches/find_hdf5_serial.patch          | 11 +++++++++++
 debian/patches/link_debian_packaged_libz.patch |  2 +-
 3 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index b0471a0..2ad19ed 100644
--- a/debian/control
+++ b/debian/control
@@ -9,6 +9,7 @@ Build-Depends: debhelper (>= 9),
                zlib1g-dev,
                libxml2-dev,
                libhdf5-dev,
+               libaec-dev,
                libmagic-dev,
                libfuse-dev,
                libngs-sdk-dev (>= 1.2.4),
diff --git a/debian/patches/find_hdf5_serial.patch b/debian/patches/find_hdf5_serial.patch
index d9f1c35..dd39662 100644
--- a/debian/patches/find_hdf5_serial.patch
+++ b/debian/patches/find_hdf5_serial.patch
@@ -9,3 +9,14 @@
          } elsif ($n eq 'fuse') {
              $flags = '-D_FILE_OFFSET_BITS=64';
              $library = '-lfuse';
+--- a/tools/pacbio-load/Makefile
++++ b/tools/pacbio-load/Makefile
+@@ -105,7 +105,7 @@ PACBIO_LOAD_LIB = \
+ 	-stk-version \
+ 	-skdf5 \
+ 	-sload \
+-	-shdf5 \
++	-shdf5_serial \
+ 	-sncbi-wvdb \
+ 	-sm \
+ 
diff --git a/debian/patches/link_debian_packaged_libz.patch b/debian/patches/link_debian_packaged_libz.patch
index 95e6a6b..88f2d41 100644
--- a/debian/patches/link_debian_packaged_libz.patch
+++ b/debian/patches/link_debian_packaged_libz.patch
@@ -10,7 +10,7 @@ Description: Since libncbi-vdb is dynamically linked against zlib and libbz2
  fi
  
 +echo "+++++++++++++++++++++++++  adding zlib +++++++++++++++++++++++++++++++++++++++"
-+CMD="$CMD -lz -lbz2"
++CMD="$CMD -lz -lbz2 -lsz"
 +
  # produce shared library
  echo $CMD

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