[med-svn] [nanopolish] 05/08: Add build dependency on libeigen3

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository nanopolish.

commit 25cbfab2aabf9ea00ebb86e28332e1d99bd2c41a
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Aug 11 20:35:00 2016 -0700

    Add build dependency on libeigen3
---
 debian/control                           |  1 +
 debian/patches/adjust-include-path.patch | 11 +++++++++++
 debian/patches/external-libs.patch       | 16 ++++++++++++++++
 debian/patches/reproducible.patch        |  2 +-
 4 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 1d28475..aa34813 100644
--- a/debian/control
+++ b/debian/control
@@ -8,6 +8,7 @@ Build-Depends:
 	zlib1g-dev,
 	libfast5-dev,
 	libhts-dev,
+	libeigen3-dev,
 Standards-Version: 3.9.8
 Homepage: https://github.com/jts/nanopolish
 Vcs-Git: https://anonscm.debian.org/git/debian-med/nanopolish.git
diff --git a/debian/patches/adjust-include-path.patch b/debian/patches/adjust-include-path.patch
index ad8836b..44ce571 100644
--- a/debian/patches/adjust-include-path.patch
+++ b/debian/patches/adjust-include-path.patch
@@ -37,3 +37,14 @@ Last-Update: 2016-08-11
  
  //
  SquiggleRead::SquiggleRead(const std::string& name, const std::string& path, const uint32_t flags) :
+--- nanopolish.orig/src/nanopolish_methyltrain.cpp
++++ nanopolish/src/nanopolish_methyltrain.cpp
+@@ -42,7 +42,7 @@
+ #include "logger.hpp"
+ 
+ #include "nanopolish_scorereads.h"
+-#include "../eigen/Eigen/Dense"
++#include <eigen3/Eigen/Dense>
+ 
+ extern float g_p_skip, g_p_skip_self, g_p_bad, g_p_bad_self;
+ 
diff --git a/debian/patches/external-libs.patch b/debian/patches/external-libs.patch
index 70fb360..3f11455 100644
--- a/debian/patches/external-libs.patch
+++ b/debian/patches/external-libs.patch
@@ -25,3 +25,19 @@ Last-Update: 2016-01-18
  
  # Include the header-only fast5 library
  FAST5_INCLUDE=-I./fast5
+@@ -68,13 +65,10 @@
+ 	cd hdf5-1.8.14; ./configure --enable-threadsafe --prefix=`pwd`/..; make; make install
+ 
+ 
+-# Download and install eigen if not already downloaded
+-EIGEN=eigen/INSTALL
++# Don't use external EIGEN
++EIGEN=
+ 
+ $(EIGEN):
+-	wget http://bitbucket.org/eigen/eigen/get/3.2.5.tar.bz2
+-	tar -xjvf 3.2.5.tar.bz2
+-	mv eigen-eigen-bdd17ee3b1b3 eigen
+ 
+ #
+ # Source files
diff --git a/debian/patches/reproducible.patch b/debian/patches/reproducible.patch
index a457fa7..a96a7f3 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -4,7 +4,7 @@ Description: make build reproducible
 Author: Sascha Steinbiss <satta at debian.org>
 --- nanopolish.orig/Makefile
 +++ nanopolish/Makefile
-@@ -78,8 +78,8 @@
+@@ -75,8 +75,8 @@
  #
  
  # Find the source files by searching subdirectories

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