Changeset: 43f84e370374 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=43f84e370374
Modified Files:
MonetDB.spec
configure.ag
debian/rules
sql/backends/monet5/Makefile.ag
sql/backends/monet5/bam/Makefile.ag
Branch: bamloader
Log Message:
Adapted .ag files, MonetDB.spec and debian/rules to look for htslib instead of
samtools
diffs (202 lines):
diff --git a/MonetDB.spec b/MonetDB.spec
--- a/MonetDB.spec
+++ b/MonetDB.spec
@@ -36,8 +36,8 @@
%define with_geos 1
%endif
-%if %{?_with_samtools:1}%{!?_with_samtools:0}
-%define with_samtools 1
+%if %{?_with_hts:1}%{!?_with_hts:0}
+%define with_hts 1
%endif
Name: %{name}
@@ -82,8 +82,8 @@ BuildRequires: rubygems-devel
%endif
BuildRequires: unixODBC-devel
BuildRequires: zlib-devel
-%if %{?with_samtools:1}%{!?with_samtools:0}
-BuildRequires: samtools-devel
+%if %{?with_hts:1}%{!?with_hts:0}
+BuildRequires: hts-devel
%endif
# need to define python_sitelib on RHEL 5 and older
@@ -456,7 +456,7 @@ numerical analysis (gsl).
%{_libdir}/monetdb5/gsl.mal
%{_libdir}/monetdb5/lib_gsl.so
-%if %{?_with_samtools:1}%{!?_with_samtools:0}
+%if %{?_with_hts:1}%{!?_with_hts:0}
%package bam-MonetDB5
Summary: MonetDB5 SQL interface to the bam library
Group: Applications/Databases
@@ -542,7 +542,7 @@ fi
%exclude %{_libdir}/monetdb5/lib_geom.so
%endif
%exclude %{_libdir}/monetdb5/lib_gsl.so
-%if %{?_with_samtools:1}%{!?_with_samtools:0}
+%if %{?_with_hts:1}%{!?_with_hts:0}
%exclude %{_libdir}/monetdb5/bam.mal
%exclude %{_libdir}/monetdb5/autoload/*_bam.mal
%exclude %{_libdir}/monetdb5/lib_bam.so
@@ -640,7 +640,7 @@ systemd-tmpfiles --create %{_sysconfdir}
%exclude %{_libdir}/monetdb5/createdb/*_geom.sql
%endif
%exclude %{_libdir}/monetdb5/createdb/*_gsl.sql
-%if %{?_with_samtools:1}%{!?_with_samtools:0}
+%if %{?_with_hts:1}%{!?_with_hts:0}
%exclude %{_libdir}/monetdb5/createdb/*_bam.sql
%endif
# %exclude %{_libdir}/monetdb5/createdb/*_rdf.sql
@@ -800,7 +800,7 @@ developer, but if you do want to test, t
--with-readline=yes \
--with-rubygem=%{?rhel:no}%{!?rhel:yes} \
--with-rubygem-dir=%{?rhel:no}%{!?rhel:"%{gem_dir}"} \
- --with-samtools=%{?with_samtools:yes}%{!?with_samtools:no} \
+ --with-hts=%{?with_hts:yes}%{!?with_hts:no} \
--with-sphinxclient=no \
--with-unixodbc=yes \
--with-valgrind=no \
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2362,49 +2362,51 @@ AC_SUBST(MSEED_CFLAGS, $MSEED_CFLAGS)
AC_SUBST(MSEED_LIBS, $MSEED_LIBS)
AM_CONDITIONAL(HAVE_MSEED, test x"$have_mseed" != xno)
-# samtools, only used by sql
-org_have_samtools="auto"
-have_samtools=$org_have_samtools
-AC_ARG_WITH(samtools,
- AS_HELP_STRING([--with-samtools=DIR],
- [samtools (providing bam library) are installed in DIR]),
- [have_samtools="$withval"], [have_samtools="auto"])
-if test "x$have_samtools" != xno; then
- case "$have_samtools" in
+# hts (required by BAM library), only used by sql
+org_have_bam="auto"
+have_bam=$org_have_bam
+AC_ARG_WITH(hts,
+ AS_HELP_STRING([--with-hts=DIR],
+ [hts (providing bam library) are installed in DIR]),
+ [have_bam="$withval"], [have_bam="auto"])
+if test "x$have_bam" != xno; then
+ case "$have_bam" in
auto|yes)
;;
*)
- SAMTOOLS_CFLAGS="-I$have_samtools/include"
- SAMTOOLS_LIBS="-L$have_samtools/lib -lbam"
+ BAM_CFLAGS="-I$have_bam/include"
+ BAM_LIBS="-L$have_bam/lib -lhts"
;;
esac
save_CPPFLAGS="$CPPFLAGS"
save_LDFLAGS="$LDFLAGS"
- CPPFLAGS="$CPPFLAGS $SAMTOOLS_CFLAGS"
- LDFLAGS="$LDFLAGS $SAMTOOLS_LIBS"
- AC_CHECK_HEADER(samtools/bam.h,
- AC_CHECK_HEADER(samtools/bgzf.h,
- AC_CHECK_LIB(bam, bam_header_read,
- AC_DEFINE(HAVE_SAMTOOLS, 1, [Define if you have
the samtools (providing the bam library)]),
- [ if test "x$have_samtools" != xauto; then
AC_MSG_ERROR([-lbam library not found]); fi
- have_samtools=no; why_have_samtools="(bam
library not found)" ],
- [-lm -lpthread -lz]),
- [ if test "x$have_samtools" != xauto; then
AC_MSG_ERROR([samtools/bgzf.h header not found]); fi
- have_samtools=no; why_have_samtools="(samtools/bgzf.h
header not found)" ]),
- [ if test "x$have_samtools" != xauto; then
AC_MSG_ERROR([samtools/bam.h header not found]); fi
- have_samtools=no; why_have_samtools="(samtools/bam.h header
not found)" ])
+ CPPFLAGS="$CPPFLAGS $BAM_CFLAGS"
+ LDFLAGS="$LDFLAGS $BAM_LIBS"
+ AC_CHECK_HEADER(htslib/sam.h,
+ AC_CHECK_HEADER(htslib/bgzf.h,
+ AC_CHECK_HEADER(htslib/kstring.h,
+ AC_CHECK_LIB(hts, sam_hdr_read,
+ AC_DEFINE(ENABLE_BAM, 1, [Define if the
BAM library will be enabled (only if htslib was found on system)]),
+ [ if test "x$have_bam" != xauto; then
AC_MSG_ERROR([-lhts library not found]); fi
+ have_bam=no; why_have_bam="(bam
library not found)" ],
+ [-lm -lpthread -lz]),
+ [ if test "x$have_bam" != xauto; then
AC_MSG_ERROR([htslib/kstring.h header not found]); fi
+ have_bam=no; why_have_bam="(htslib/kstring.h
header not found)" ]),
+ [ if test "x$have_bam" != xauto; then
AC_MSG_ERROR([htslib/bgzf.h header not found]); fi
+ have_bam=no; why_have_bam="(htslib/bgzf.h header not
found)" ]),
+ [ if test "x$have_bam" != xauto; then
AC_MSG_ERROR([htslib/sam.h header not found]); fi
+ have_bam=no; why_have_bam="(htslib/sam.h header not found)" ])
LDFLAGS="$save_LDFLAGS"
CPPFLAGS="$save_CPPFLAGS"
- if test "x$have_samtools" = "xyes" -o "x$have_samtools" = "xauto"; then
- SAMTOOLS_CFLAGS=
- SAMTOOLS_LIBS="-lbam"
- AC_CHECK_HEADERS([samtools/kstring.h])
+ if test "x$have_bam" = "xyes" -o "x$have_bam" = "xauto"; then
+ BAM_CFLAGS=
+ BAM_LIBS="-lhts"
fi
fi
-AC_SUBST(SAMTOOLS_CFLAGS, $SAMTOOLS_CFLAGS)
-AC_SUBST(SAMTOOLS_LIBS, $SAMTOOLS_LIBS)
-AM_CONDITIONAL(HAVE_SAMTOOLS, test x"$have_samtools" != xno)
+AC_SUBST(BAM_CFLAGS, $BAM_CFLAGS)
+AC_SUBST(BAM_LIBS, $BAM_LIBS)
+AM_CONDITIONAL(ENABLE_BAM, test x"$have_bam" != xno)
# geos, only used in geom module
org_have_geos=auto
@@ -3447,7 +3449,7 @@ for comp in \
'raptor ' \
'readline ' \
'rubygem ' \
- 'samtools ' \
+ 'bam ' \
'setsockopt ' \
'sphinxclient ' \
'unixodbc ' \
diff --git a/debian/rules b/debian/rules
--- a/debian/rules
+++ b/debian/rules
@@ -60,7 +60,7 @@ override_dh_auto_configure:
--with-readline=yes \
--with-rubygem=yes \
--with-rubygem-dir=lib/ruby/gems/1.8 \
- --with-samtools=yes \
+ --with-hts=yes \
--with-sphinxclient=no \
--with-unixodbc=yes \
--with-valgrind=no
diff --git a/sql/backends/monet5/Makefile.ag b/sql/backends/monet5/Makefile.ag
--- a/sql/backends/monet5/Makefile.ag
+++ b/sql/backends/monet5/Makefile.ag
@@ -15,7 +15,7 @@
# Copyright August 2008-2014 MonetDB B.V.
# All Rights Reserved.
-SUBDIRS = NOT_WIN32?vaults UDF HAVE_SAMTOOLS?bam LSST ENABLE_DATACELL?datacell
HAVE_JSONSTORE?rest HAVE_GSL?gsl
+SUBDIRS = NOT_WIN32?vaults UDF ENABLE_BAM?bam LSST ENABLE_DATACELL?datacell
HAVE_JSONSTORE?rest HAVE_GSL?gsl
INCLUDES = ../../include ../../common ../../storage ../../server \
../../../monetdb5/modules/atoms \
diff --git a/sql/backends/monet5/bam/Makefile.ag
b/sql/backends/monet5/bam/Makefile.ag
--- a/sql/backends/monet5/bam/Makefile.ag
+++ b/sql/backends/monet5/bam/Makefile.ag
@@ -30,7 +30,8 @@ INCLUDES = .. \
../../../../common/stream \
../../../../gdk \
../../../../tools/merovingian \
- ../../../../tools/merovingian/daemon
+ ../../../../tools/merovingian/daemon \
+ $(BAM_CFLAGS)
lib__bam = {
MODULE
@@ -43,7 +44,7 @@ lib__bam = {
bam_export.c bam_export.h
LIBS = ../../../../monetdb5/tools/libmonetdb5 \
../../../../gdk/libbat \
- -lhts
+ $(BAM_LIBS)
}
headers_mal = {
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