[med-svn] [sra-sdk] 04/04: Now at least ngs-sdk is found, needs packaging of https://github.com/ncbi/ncbi-vdb

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository sra-sdk.

commit 92050d935b4be43dddc20fd12eb12be802db9108
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 15 14:13:01 2016 +0200

    Now at least ngs-sdk is found, needs packaging of https://github.com/ncbi/ncbi-vdb
---
 debian/changelog                  |  2 ++
 debian/patches/find_ngs-sdk.patch | 50 +++++++++++++++++++++++++++++++++++++++
 debian/rules                      |  2 +-
 3 files changed, 53 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 6e1f9f9..6cfe65b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,7 @@
 sra-sdk (2.6.3-1) UNRELEASED; urgency=medium
 
+  TODO: packaging of https://github.com/ncbi/ncbi-vdb
+
   [ Andreas Tille ]
   * New upstream version
   * d/watch points to github
diff --git a/debian/patches/find_ngs-sdk.patch b/debian/patches/find_ngs-sdk.patch
new file mode 100644
index 0000000..c0b2199
--- /dev/null
+++ b/debian/patches/find_ngs-sdk.patch
@@ -0,0 +1,50 @@
+--- a/setup/konfigure.perl
++++ b/setup/konfigure.perl
+@@ -439,6 +439,7 @@ if ($TOOLS =~ /gcc$/) {
+ 
+ my @dependencies;
+ 
++$OPT{'debug'} = 1;
+ my %DEPEND_OPTIONS;
+ foreach my $href (DEPENDS()) {
+     $_ = $href->{name};
+@@ -936,7 +937,7 @@ EndText
+ 
+     if ($PKG{LNG} eq 'JAVA') {
+         L($F,
+-            "INCPATHS = \$(SRCDIR):\$(SRCDIR)/itf:\$(TOP)/gov/nih/nlm/ncbi/ngs")
++            "INCPATHS = \$(SRCDIR):/usr/include/ngs/itf:/usr/include/ngs")
+     }
+ 
+     print $F <<EndText;
+@@ -1314,7 +1315,9 @@ sub find_in_dir {
+         print "\tlibraries... " unless ($AUTORUN);
+         if ($lib) {
+             my $builddir = File::Spec->catdir($dir, $OS, $TOOLS, $ARCH, $BUILD);
+-            my $libdir  = File::Spec->catdir($builddir, 'lib');
++            my $buildarch = `dpkg-architecture -qDEB_BUILD_MULTIARCH`;
++            chomp $buildarch;
++            my $libdir  = File::Spec->catdir($dir, 'lib', $buildarch);
+             my $ilibdir = File::Spec->catdir($builddir, 'ilib');
+             my $f = File::Spec->catdir($libdir, $lib);
+             print "\n\t\tchecking $f\n\t" if ($OPT{'debug'});
+--- a/setup/package.prl
++++ b/setup/package.prl
+@@ -8,7 +8,7 @@ sub CONFIG_OUT   { 'build' }
+ sub PKG { ( LNG   => 'C',
+             OUT   => 'ncbi-outdir',
+             LOCOUT=> '../../OUTDIR',
+-            PATH  => '/usr/local/ncbi/sra-tools',
++            PATH  => '/usr/bin/sra-tools',
+             UPATH =>      '$HOME/ncbi/sra-tools', ) }
+ sub DEPENDS { ( { name => 'fuse' , Include => '/usr/include'        , },
+                 { name => 'hdf5' , Include => '/usr/include'        , },
+@@ -20,7 +20,7 @@ sub REQ { (
+               option  => 'with-ngs-sdk-prefix',
+               origin  => 'I',
+               type    => 'L',
+-              srcpath => '../ngs/ngs-sdk',
++              srcpath => '/usr/include',
+               pkgpath => '/usr/local/ngs/ngs-sdk',
+               usrpath =>      '$HOME/ngs/ngs-sdk',
+               bldpath => '$HOME/ncbi-outdir/ngs-sdk',
diff --git a/debian/rules b/debian/rules
index ce8d236..26ead17 100755
--- a/debian/rules
+++ b/debian/rules
@@ -16,7 +16,7 @@ override_dh_update_autotools_config:
 
 override_dh_auto_configure:
         # that's no standard configure script lacking support of default options
-	./configure --build=$(BUILDTYPE) --prefix=/usr --with-ngs-sdk-prefix=/usr
+	./configure --build=$(BUILDTYPE) --prefix=/usr --build-prefix=$(CURDIR)/debian/tmp/usr --with-ngs-sdk-prefix=/usr --with-debug
 
 override_dh_auto_build:
 	export LD_LIBRARY_PATH="$$LD_LIBRARY_PATH:$(OUTDIR)/lib"; export OUTDIR=$(OUTDIR) ; make DEB_CFLAGS="$(CFLAGS)" DEB_LDFLAGS="$(LDFLAGS)"

-- 
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