[med-svn] [mugsy] 01/01: Some seqan adaptions - now we are running in serious C++ errors where I need help to solve ...

[Andreas Tille]

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tille pushed a commit to branch master
in repository mugsy.

commit 4c4040f1d6ae21ea869252b6bb3cf53bb3c71750
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 15 09:33:18 2015 +0200

    Some seqan adaptions - now we are running in serious C++ errors where I need help to solve ...
---
 debian/control                   |  3 ++-
 debian/patches/mugsy-seqan.patch | 22 ++++++++++++++++++++++
 debian/patches/series            |  1 +
 3 files changed, 25 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 481ea7b..e48949c 100644
--- a/debian/control
+++ b/debian/control
@@ -4,7 +4,8 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               libboost-dev
+               libboost-dev,
+               seqan-dev
 Standards-Version: 3.9.6
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mugsy.git
 Vcs-Git: git://anonscm.debian.org/debian-med/mugsy.git
diff --git a/debian/patches/mugsy-seqan.patch b/debian/patches/mugsy-seqan.patch
new file mode 100644
index 0000000..8c9c8f5
--- /dev/null
+++ b/debian/patches/mugsy-seqan.patch
@@ -0,0 +1,22 @@
+--- a/Makefile
++++ b/Makefile
+@@ -16,7 +16,7 @@ synchain_mugsy:
+ 	make -C chaining synchain-mugsy
+ 
+ mugsy_seqan:
+-	make -C mugsy-seqan Project=mugsy
++	make -C mugsy-seqan/projects/library/apps
+ 
+ mugsy_install:
+ 	mkdir -p ${INSTALL_DIR}
+--- a/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
++++ b/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp
+@@ -31,7 +31,7 @@ time_t lasttime;
+ #include <seqan/graph_types.h>
+ #include <seqan/graph_align.h>
+ #include <seqan/modifier.h>
+-#include <seqan/refinement.h>
++#include <seqan/graph_msa/graph_align_tcoffee_refinement.h>
+ 
+ #include "rna_alphabet.h"
+ #include <seqan/modifier.h>
diff --git a/debian/patches/series b/debian/patches/series
index ea50bd4..1d0b89f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 use_debian_packaged_mummer.patch
 adapt_to_latest_boost_version.patch
 libboost_linking.patch
+mugsy-seqan.patch

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