[med-svn] [Git][med-team/libucsc][master] Add missing Build-Depends, use Debian packaged htslib

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / libucsc


Commits:
f4c03128 by Andreas Tille at 2018-05-19T14:00:09+02:00
Add missing Build-Depends, use Debian packaged htslib

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/series
- + debian/patches/use_debian_packaged_htslib.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,4 +4,4 @@ libucsc (0.0+git20180518.91029f67+dfsg-1) UNRELEASED; urgency=medium
   Does not build:
     https://github.com/ucscGenomeBrowser/kent/issues/13
 
- -- Andreas Tille <tille at debian.org>  Tue, 05 Jul 2016 15:09:25 +0200
+ -- Andreas Tille <tille at debian.org>  Sat, 19 May 2018 13:59:04 +0200


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
+Build-Depends: debhelper (>= 11~),
+               libhts-dev,
+               libssl-dev
 Standards-Version: 4.1.4
 Vcs-Browser: https://salsa.debian.org/med-team/libucsc
 Vcs-Git: https://salsa.debian.org/med-team/libucsc.git


=====================================
debian/patches/series
=====================================
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_htslib.patch


=====================================
debian/patches/use_debian_packaged_htslib.patch
=====================================
--- /dev/null
+++ b/debian/patches/use_debian_packaged_htslib.patch
@@ -0,0 +1,57 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 19 May 2018 13:59:04 +0200
+Description: Use Debian packaged htslib
+
+--- a/src/inc/bamFile.h
++++ b/src/inc/bamFile.h
+@@ -11,7 +11,7 @@
+ #ifndef _IOLIB
+ #define _IOLIB 2
+ #endif
+-#include "htslib/sam.h"
++#include <htslib/sam.h>
+ typedef samFile samfile_t;
+ typedef hts_idx_t bam_index_t;
+ typedef bam_hdr_t bam_header_t;
+--- a/src/inc/common.mk
++++ b/src/inc/common.mk
+@@ -18,7 +18,7 @@ ifneq (,$(findstring -,$(MACHTYPE)))
+ endif
+ 
+ HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
+-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
++HG_INC+=-I../inc 
+ 
+ # to check for Mac OSX Darwin specifics:
+ UNAME_S := $(shell uname -s)
+@@ -259,7 +259,7 @@ ifeq (${ZLIB},)
+ endif
+ 
+ #global external libraries
+-L += $(kentSrc)/htslib/libhts.a
++L += -lhts
+ 
+ L+=${PNGLIB} ${ZLIB} ${MLIB}
+ HG_INC+=${PNGINCL}
+--- a/src/lib/knetUdc.c
++++ b/src/lib/knetUdc.c
+@@ -8,7 +8,7 @@
+ #include "common.h"
+ #include "udc.h"
+ #include "knetUdc.h"
+-#include "htslib/knetfile.h"
++#include <htslib/knetfile.h>
+ 
+ static char *udcCacheDir = NULL;
+ 
+--- a/src/lib/linefile.c
++++ b/src/lib/linefile.c
+@@ -15,7 +15,7 @@
+ #include "localmem.h"
+ #include "cheapcgi.h"
+ #include "udc.h"
+-#include "htslib/tbx.h"
++#include <htslib/tbx.h>
+ 
+ char *getFileNameFromHdrSig(char *m)
+ /* Check if header has signature of supported compression stream,


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -16,7 +16,4 @@ include /usr/share/dpkg/default.mk
 # export DEB_BUILD_MAINT_OPTIONS=hardening=+all
 
 %:
-	dh $@
-
-#get-orig-source:
-#	. debian/get-orig-source
+	dh $@ --sourcedirectory=src/lib



View it on GitLab: https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016

---
View it on GitLab: https://salsa.debian.org/med-team/libucsc/commit/f4c0312891721f36cd4354389fbd0bd9ce4da016
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