Add missing Build-Depends, use Debian packaged htslib (f4c03128) · Commits · Debian Med / libucsc

debian/changelog

+1 −1

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		@@ -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@debian.org> Tue, 05 Jul 2016 15:09:25 +0200
		-- Andreas Tille <tille@debian.org> Sat, 19 May 2018 13:59:04 +0200

+3 −1

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		@@ -3,7 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
		Uploaders: Andreas Tille <tille@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

0 → 100644

+1 −0

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		use_debian_packaged_htslib.patch

0 → 100644

+57 −0

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		Author: Andreas Tille <tille@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,

+1 −4

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		@@ -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