Changeset: c2cb389ff8d1 for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=c2cb389ff8d1
Modified Files:
NT/monetdb_config.h.in
NT/rules.msc
configure.ag
sql/backends/monet5/Makefile.ag
sql/backends/monet5/bam/Makefile.ag
sql/backends/monet5/bam/README
testing/Mtest.py.in
Branch: DVframework_bam
Log Message:
use configure (via --with-samtools=...) to find samtools,
and compile sql/backends/monet5/bam/ only if samtools were found.
This is more convenient than editing
sql/backends/monet5/bam/Makefile.ag
by hand ...
diffs (163 lines):
diff --git a/NT/monetdb_config.h.in b/NT/monetdb_config.h.in
--- a/NT/monetdb_config.h.in
+++ b/NT/monetdb_config.h.in
@@ -386,6 +386,9 @@
/* Define to 1 if you have the `round' function. */
/* #undef HAVE_ROUND */
+/* Define if you have the samtools (providing the bam library) */
+/* #undef HAVE_SAMTOOLS */
+
/* Define to 1 if you have the `sbrk' function. */
/* #undef HAVE_SBRK */
diff --git a/NT/rules.msc b/NT/rules.msc
--- a/NT/rules.msc
+++ b/NT/rules.msc
@@ -391,6 +391,11 @@ create_winconfig_conds_new_py:
!ELSE
$(ECHO) HAVE_RUBYGEM_FALSE='' >> "$(TOPDIR)\winconfig_conds_new.py"
!ENDIF
+!IFDEF HAVE_SAMTOOLS
+ $(ECHO) HAVE_SAMTOOLS_FALSE='#' >> "$(TOPDIR)\winconfig_conds_new.py"
+!ELSE
+ $(ECHO) HAVE_SAMTOOLS_FALSE='' >> "$(TOPDIR)\winconfig_conds_new.py"
+!ENDIF
!IFDEF HAVE_SPHINXCLIENT
$(ECHO) HAVE_SPHINXCLIENT_FALSE='#' >>
"$(TOPDIR)\winconfig_conds_new.py"
!ELSE
diff --git a/configure.ag b/configure.ag
--- a/configure.ag
+++ b/configure.ag
@@ -2209,6 +2209,45 @@ 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
+have_samtools="auto"
+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 "$have_samtools" in
+ auto|yes)
+ ;;
+ *)
+ SAMTOOLS_CFLAGS="-I$have_samtools/include"
+ SAMTOOLS_LIBS="-L$have_samtools/lib -lbam"
+ ;;
+ esac
+
+ save_CPPFLAGS="$CPPFLAGS"
+ save_LDFLAGS="$LDFLAGS"
+ CPPFLAGS="$CPPFLAGS $SAMTOOLS_CFLAGS"
+ LDFLAGS="$LDFLAGS $SAMTOOLS_LIBS"
+ AC_CHECK_HEADER(bam.h,
+ AC_CHECK_HEADER(bgzf.h,
+ AC_CHECK_LIB(bam, bam_header_read,
+ AC_DEFINE(HAVE_SAMTOOLS, 1, [Define if you have
the samtools (providing the bam library)]),
+ [ if test "x$have_samtoouls" != xauto; then
AC_MSG_ERROR([-lbam library not found]); fi; have_samtools=no ],
+ [-lpthread -lz]),
+ [ if test "x$have_samtools" != xauto; then
AC_MSG_ERROR([bgzf.h header not found]); fi; have_samtools=no ]),
+ [ if test "x$have_samtools" != xauto; then AC_MSG_ERROR([bam.h
header not found]); fi; have_samtools=no ])
+ LDFLAGS="$save_LDFLAGS"
+ CPPFLAGS="$save_CPPFLAGS"
+ if test "x$have_samtools" = "xyes" -o "x$have_samtools" = "xauto"; then
+ SAMTOOLS_CFLAGS=
+ SAMTOOLS_LIBS="-lbam"
+ fi
+fi
+AC_SUBST(SAMTOOLS_CFLAGS, $SAMTOOLS_CFLAGS)
+AC_SUBST(SAMTOOLS_LIBS, $SAMTOOLS_LIBS)
+AM_CONDITIONAL(HAVE_SAMTOOLS, test x"$have_samtools" != xno)
+
# geos, only used in geom module
have_geos=auto
GEOS_INCS=''
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 2008-2013 MonetDB B.V.
# All Rights Reserved.
-SUBDIRS = NOT_WIN32?vaults UDF bam LSST ENABLE_DATACELL?datacell
HAVE_MSEED?miniseed
+SUBDIRS = NOT_WIN32?vaults UDF HAVE_SAMTOOLS?bam LSST ENABLE_DATACELL?datacell
HAVE_MSEED?miniseed
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
@@ -29,7 +29,7 @@ INCLUDES = .. \
../../../../common/options \
../../../../common/stream \
../../../../gdk \
- -I$(HOME)/Documents/BAM/samtools/include
+ $(SAMTOOLS_CFLAGS)
lib__bam = {
MODULE
@@ -37,8 +37,7 @@ lib__bam = {
SOURCES = bamloader.c bamloader.h
LIBS = ../../../../monetdb5/tools/libmonetdb5 \
../../../../gdk/libbat \
- -L$(HOME)/Documents/BAM/samtools/lib -lbam
-
+ $(SAMTOOLS_LIBS)
}
headers_mal = {
diff --git a/sql/backends/monet5/bam/README b/sql/backends/monet5/bam/README
--- a/sql/backends/monet5/bam/README
+++ b/sql/backends/monet5/bam/README
@@ -4,26 +4,30 @@ This document describes how to use the c
***************************************************************************************************
Installation
***************************************************************************************************
-In order to run the code, samtools has to be installed. To do so, create a
directory named
+In order to run the code, samtools [1][2] has to be installed. To do so,
create a directory named
samtools in some location <samtools_location> and unpack the contents of
samtools into
<samtools_location>/samtools. Then, create symbolic links
<samtools_location>/lib and
<samtools_location>/include that both link to <samtools_location>/samtools.
Now install
samtools with the compiler flag -fPIC (in my case, I had to alter the by
samtools provided
Makefile by setting the constant CFLAGS to -g -Wall -O2 -fPIC.
-In order to link samtools to MonetDB, edit sql/backends/monet5/bam/Makefile.ag
by changing
-$(HOME)/Documents/BAM/ to <samtools_location>.
-
The bamloader writes messages to a log file. For now, this logfile is
specified in sql/
backends/monet5/bam/bamloader.h in the constant LOG_FILE. Change this to a
filepath of
choice. The given directory must exist, while the file does not. If the file
doesn't
exist it is automatically created.
-That should be enough to compile and install MonetDB. Do so by running the
bootstrap,
-configure, make and make install steps described on
-http://www.monetdb.org/wiki/MonetDB:Building_from_sources
+Then you can compile and install MonetDB with BAM file support using the usual
sequence
+as described at http://www.monetdb.org/wiki/MonetDB:Building_from_sources ,
+but telling configure where to find your samtools installation, i.e.,
+ bootstrap
+ configure --with-samtools=<samtools_location>
+ make
+ make install
+[1] http://samtools.sourceforge.net/
+[2] http://en.wikipedia.org/wiki/SAMtools
+
***************************************************************************************************
Loading BAM files in the database
diff --git a/testing/Mtest.py.in b/testing/Mtest.py.in
--- a/testing/Mtest.py.in
+++ b/testing/Mtest.py.in
@@ -329,6 +329,7 @@ CONDITIONALS = {
'HAVE_PYTHON3' : "@HAVE_PYTHON3_FALSE@",
'HAVE_RAPTOR' : "@HAVE_RAPTOR_FALSE@",
'HAVE_RUBYGEM' : "@HAVE_RUBYGEM_FALSE@",
+ 'HAVE_SAMTOOLS' : "@HAVE_SAMTOOLS_FALSE@",
'HAVE_SPHINXCLIENT' : "@HAVE_SPHINXCLIENT_FALSE@",
'HAVE_SQL' : "@HAVE_SQL_FALSE@",
'HAVE_TESTING' : "@HAVE_TESTING_FALSE@",
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