[med-svn] [pbbam] 01/06: Add libssl dependency and missing linker flags to allow package build

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository pbbam.

commit 129b08efe6069266d0bcba5341e2ea2fe9225893
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Sep 7 21:06:52 2015 -0700

    Add libssl dependency and missing linker flags to allow package build
---
 debian/control         |  1 +
 debian/patches/series  |  1 +
 debian/patches/ssl-md5 | 24 ++++++++++++++++++++++++
 debian/rules           |  3 ++-
 4 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index c5d8ede..e750bd8 100644
--- a/debian/control
+++ b/debian/control
@@ -9,6 +9,7 @@ Build-Depends: debhelper (>= 9),
 	       doxygen,
 	       libboost-dev (>= 1.54),
 	       zlib1g-dev,
+	       libssl-dev,
 	       libhts-dev,
 	       samtools
 Standards-Version: 3.9.6
diff --git a/debian/patches/series b/debian/patches/series
index 1a37804..f3a7560 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 set-samtools-path
+ssl-md5
diff --git a/debian/patches/ssl-md5 b/debian/patches/ssl-md5
new file mode 100644
index 0000000..af927ec
--- /dev/null
+++ b/debian/patches/ssl-md5
@@ -0,0 +1,24 @@
+Description: Use libssl for md5.h rather than cram
+ cram/md5.h was part of HTSlib [1] (seems to have been removed in the current
+ development tree), but those headers are not installed by that
+ package's build system. md5.h in particular has a very generic function,
+ served apparently by libssl. Furthermore, the cram/* headers are not intended
+ to be used directly [2]. This patch uses libssl to provide md5.h for this
+ package.
+ .
+ 1. https://anonscm.debian.org/cgit/debian-med/htslib.git/tree/cram/md5.h?id=12251926b9d0265738d701bb0add6fe9d070ccb3
+ 2. http://sourceforge.net/p/samtools/mailman/message/33488076/
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: no
+Last-Update: 2015-09-07
+--- pbbam.orig/src/ReadGroupInfo.cpp
++++ pbbam/src/ReadGroupInfo.cpp
+@@ -37,7 +37,7 @@
+ 
+ #include "pbbam/ReadGroupInfo.h"
+ #include "SequenceUtils.h"
+-#include <cram/md5.h>
++#include <openssl/md5.h>
+ #include <cstdio>
+ #include <set>
+ #include <sstream>
diff --git a/debian/rules b/debian/rules
index 1a9b4a7..c12d579 100755
--- a/debian/rules
+++ b/debian/rules
@@ -14,6 +14,7 @@ override_dh_auto_configure:
 	-DPacBioBAM_build_tests=OFF \
 	-DCMAKE_LIBRARY_PATH=$(DEB_HOST_MULTIARCH) \
 	-DHTSLIB_INCLUDE_DIRS=/usr/include \
-	-DHTSLIB_LIBRARIES=/usr/lib
+	-DHTSLIB_LIBRARIES=/usr/lib \
+	-DCMAKE_SHARED_LINKER_FLAGS="-lssl -lhts"
 #	-DPacBioBAM_wrap_python=ON \
 #	-DPacBioBAM_wrap_r=ON

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