[med-svn] [pbdagcon] 08/12: Build dazcon

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository pbdagcon.

commit 77d4560d99993dd0777d7d92efec663c1d8b8f01
Author: Afif Elghraoui <afif at debian.org>
Date:   Wed Dec 21 00:20:52 2016 -0800

    Build dazcon
---
 debian/TODO                 |  1 -
 debian/install              |  1 +
 debian/patches/dazcon.patch | 16 ----------------
 debian/patches/series       |  1 -
 debian/rules                |  3 +++
 5 files changed, 4 insertions(+), 18 deletions(-)

diff --git a/debian/TODO b/debian/TODO
deleted file mode 100644
index b781f2b..0000000
--- a/debian/TODO
+++ /dev/null
@@ -1 +0,0 @@
-* Bundle upstream's forks of DAZZDB and DALIGNER (as included in submodules) in order to build dazcon
diff --git a/debian/install b/debian/install
index 4a0c2e5..0d991d6 100644
--- a/debian/install
+++ b/debian/install
@@ -1 +1,2 @@
 src/cpp/pbdagcon usr/bin
+src/cpp/dazcon usr/bin
diff --git a/debian/patches/dazcon.patch b/debian/patches/dazcon.patch
deleted file mode 100644
index b5aa374..0000000
--- a/debian/patches/dazcon.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: Exclude dazcon from the build for now
- The source tarball needs to bundle the PacBio fork of DALIGNER and DAZZDB
- in order to build dazcon. We'll have to do that later.
-Author: Afif Elghraoui <afif at debian.org>
-Forwarded: not-needed
---- pbdagcon.orig/src/cpp/makefile
-+++ pbdagcon/src/cpp/makefile
-@@ -50,7 +50,7 @@
- vpath DB.c ${DAZZ_DB_SRC}
- vpath QV.c ${DAZZ_DB_SRC}
- 
--all: pbdagcon dazcon
-+all: pbdagcon
- 
- # Technically does not need pbdata or blasr, but so what?
- dazcon: $(COMMON_OBJECTS) $(DAZCON_OBJECTS)
diff --git a/debian/patches/series b/debian/patches/series
index 8f61f3d..a4675fc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1 @@
 compiler-flags.patch
-dazcon.patch
diff --git a/debian/rules b/debian/rules
index 5d4f513..0891fbf 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,6 +11,9 @@ export LIBPBDATA_INC=$(PBSEQ_BASE)/pbdata
 export LIBPBIHDF_INC=$(PBSEQ_BASE)/hdf
 export HDF5_LIB = /usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
 
+export DALIGNER_SRC = $(CURDIR)/DALIGNER
+export DAZZ_DB_SRC = $(CURDIR)/DAZZ_DB
+
 export DEB_CPPFLAGS_MAINT_APPEND = -I$(LIBBLASR_INC) -I$(LIBPBDATA_INC) -I$(LIBPBIHDF_INC)
 
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