new file: DESCR new file: Makefile new file: PLIST new file: distinfo new file: patches/patch-ngs-bam_setup_konfigure.perl new file: patches/patch-ngs-java_setup_konfigure.perl new file: patches/patch-ngs-python_setup_konfigure.perl new file: patches/patch-ngs-sdk_setup_konfigure.perl

[zmsaif <zmsaif%nmsu.edu@localhost>]

Module Name:	pkgsrc-wip
Committed By:	zmsaif <zmsaif%nmsu.edu@localhost>
Pushed By:	zmsaif
Date:		Tue Jun 27 12:05:31 2017 -0600
Changeset:	20e2266773ebbfab0aa36bfec1bf3c10d2ff073a

Added Files:
	ngs-sdk-all/DESCR
	ngs-sdk-all/Makefile
	ngs-sdk-all/PLIST
	ngs-sdk-all/distinfo
	ngs-sdk-all/patches/patch-ngs-bam_setup_konfigure.perl
	ngs-sdk-all/patches/patch-ngs-java_setup_konfigure.perl
	ngs-sdk-all/patches/patch-ngs-python_setup_konfigure.perl
	ngs-sdk-all/patches/patch-ngs-sdk_setup_konfigure.perl

Log Message:
	new file:   DESCR
	new file:   Makefile
	new file:   PLIST
	new file:   distinfo
	new file:   patches/patch-ngs-bam_setup_konfigure.perl
	new file:   patches/patch-ngs-java_setup_konfigure.perl
	new file:   patches/patch-ngs-python_setup_konfigure.perl
	new file:   patches/patch-ngs-sdk_setup_konfigure.perl

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=20e2266773ebbfab0aa36bfec1bf3c10d2ff073a

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 ngs-sdk-all/DESCR                                  |  0
 ngs-sdk-all/Makefile                               | 33 ++++++++++++++++
 ngs-sdk-all/PLIST                                  |  1 +
 ngs-sdk-all/distinfo                               | 10 +++++
 .../patches/patch-ngs-bam_setup_konfigure.perl     | 46 ++++++++++++++++++++++
 .../patches/patch-ngs-java_setup_konfigure.perl    | 46 ++++++++++++++++++++++
 .../patches/patch-ngs-python_setup_konfigure.perl  | 46 ++++++++++++++++++++++
 .../patches/patch-ngs-sdk_setup_konfigure.perl     | 46 ++++++++++++++++++++++
 8 files changed, 228 insertions(+)

diffs:
diff --git a/ngs-sdk-all/DESCR b/ngs-sdk-all/DESCR
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/ngs-sdk-all/Makefile b/ngs-sdk-all/Makefile
new file mode 100644
index 0000000000..215b11456d
--- /dev/null
+++ b/ngs-sdk-all/Makefile
@@ -0,0 +1,33 @@
+# $NetBSD$
+
+GITHUB_PROJECT=	ngs
+DISTNAME=	1.2.3
+PKGNAME=	ngs-sdk-all-${DISTNAME}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=ncbi/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
+
+MAINTAINER=	INSERT_YOUR_MAIL_ADDRESS_HERE
+HOMEPAGE=	${MASTER_SITE_GITHUB:=ncbi/ngs/}
+COMMENT=	TODO: Short description of the package
+#LICENSE=	# TODO: (see mk/license.mk)
+.include "../../biology/ngs-sdk/buildlink3.mk"
+
+#DEPENDS+=	ngs-sdk
+WRKSRC=		${WRKDIR}/${GITHUB_PROJECT}-${DISTNAME}
+HAS_CONFIGURE=	yes
+CONFIGURE_ARGS+=	--prefix=${PREFIX}
+USE_TOOLS+=	gmake perl:build
+USE_LANGUAGES=	c c++
+BUILD_TARGET=	default
+.include "../../mk/java-vm.mk"
+.include "../../mk/bsd.pkg.mk"
+repatch:
+	mkpatches
+	${MAKE} mps
+	${MAKE} clean
+	${MAKE} configure
+
+remake:
+	${MAKE} clean
+	${MAKE} configure
diff --git a/ngs-sdk-all/PLIST b/ngs-sdk-all/PLIST
new file mode 100644
index 0000000000..48d96a5493
--- /dev/null
+++ b/ngs-sdk-all/PLIST
@@ -0,0 +1 @@
+@comment $NetBSD$
diff --git a/ngs-sdk-all/distinfo b/ngs-sdk-all/distinfo
new file mode 100644
index 0000000000..ad6882bc38
--- /dev/null
+++ b/ngs-sdk-all/distinfo
@@ -0,0 +1,10 @@
+$NetBSD$
+
+SHA1 (ngs/1.2.3.tar.gz) = 2972484bf163b3678d73dd455a26ec794d8b4170
+RMD160 (ngs/1.2.3.tar.gz) = f5992f0f2a2aaae391353f645d084bbd9367e766
+SHA512 (ngs/1.2.3.tar.gz) = 24edd00a8ca80aaa2d76c512841d6f462d2b7598f518fe961e2e4d78799044b09e0bc828b8789704fd4301469896fe0abafd4b2f5e0a3bae43bbaef9487b6297
+Size (ngs/1.2.3.tar.gz) = 977970 bytes
+SHA1 (patch-ngs-bam_setup_konfigure.perl) = 3f5025dfb96f31a99eb1d42555bb9a72d66c69fe
+SHA1 (patch-ngs-java_setup_konfigure.perl) = 4fbae9e5ff4ef19f26a958cc847f28d0122870f9
+SHA1 (patch-ngs-python_setup_konfigure.perl) = 719a057797547d7f8ea9bb592991686d6bdaab10
+SHA1 (patch-ngs-sdk_setup_konfigure.perl) = 5d0525df214a4c3caca9dff14e41aeb7fb4fc955
diff --git a/ngs-sdk-all/patches/patch-ngs-bam_setup_konfigure.perl b/ngs-sdk-all/patches/patch-ngs-bam_setup_konfigure.perl
new file mode 100644
index 0000000000..5479a4cd42
--- /dev/null
+++ b/ngs-sdk-all/patches/patch-ngs-bam_setup_konfigure.perl
@@ -0,0 +1,46 @@
+$NetBSD$
+
+--- ngs-bam/setup/konfigure.perl.orig	2015-11-23 18:38:45.000000000 +0000
++++ ngs-bam/setup/konfigure.perl
+@@ -198,14 +198,14 @@ print "checking system type... " unless
+ my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
+ println $OSTYPE unless ($AUTORUN);
+ 
+-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'NetBSD') {
+     println "configure: error: unsupported system '$OSTYPE'";
+     exit 1;
+ }
+ 
+ print "checking machine architecture... " unless ($AUTORUN);
+ println $MARCH unless ($AUTORUN);
+-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
++unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /amd64/i) {
+     println "configure: error: unsupported architecture '$OSTYPE'";
+     exit 1;
+ }
+@@ -300,6 +300,8 @@ if ($MARCH =~ /x86_64/i) {
+     $BITS = '32_64';
+ } elsif ($MARCH =~ /i?86/i) {
+     $BITS = 32;
++} elsif ($MARCH =~ /amd64/i) {
++    $BITS = 64;
+ } else {
+     die "unrecognized Architecture '$ARCH'";
+ }
+@@ -329,6 +331,15 @@ if ($OSTYPE =~ /linux/i) {
+     $TOOLS = 'clang' unless ($TOOLS);
+ } elsif ($OSTYPE eq 'win') {
+     $TOOLS = 'vc++';
++} elsif ($OSTYPE =~ /NetBSD/i) {
++    $LPFX = 'lib';
++    $OBJX = 'o';
++    $LOBX = 'pic.o';
++    $LIBX = 'a';
++    $SHLX = 'so';
++    $EXEX = '';
++    $OSINC = 'unix';
++    $TOOLS = 'gcc' unless ($TOOLS);
+ } else {
+     die "unrecognized OS '$OSTYPE'";
+ }
diff --git a/ngs-sdk-all/patches/patch-ngs-java_setup_konfigure.perl b/ngs-sdk-all/patches/patch-ngs-java_setup_konfigure.perl
new file mode 100644
index 0000000000..91b937e043
--- /dev/null
+++ b/ngs-sdk-all/patches/patch-ngs-java_setup_konfigure.perl
@@ -0,0 +1,46 @@
+$NetBSD$
+
+--- ngs-java/setup/konfigure.perl.orig	2015-11-23 18:38:45.000000000 +0000
++++ ngs-java/setup/konfigure.perl
+@@ -198,14 +198,14 @@ print "checking system type... " unless
+ my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
+ println $OSTYPE unless ($AUTORUN);
+ 
+-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'NetBSD') {
+     println "configure: error: unsupported system '$OSTYPE'";
+     exit 1;
+ }
+ 
+ print "checking machine architecture... " unless ($AUTORUN);
+ println $MARCH unless ($AUTORUN);
+-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
++unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /amd64/i) {
+     println "configure: error: unsupported architecture '$OSTYPE'";
+     exit 1;
+ }
+@@ -300,6 +300,8 @@ if ($MARCH =~ /x86_64/i) {
+     $BITS = '32_64';
+ } elsif ($MARCH =~ /i?86/i) {
+     $BITS = 32;
++} elsif ($MARCH =~ /amd64/i) {
++    $BITS = 64;
+ } else {
+     die "unrecognized Architecture '$ARCH'";
+ }
+@@ -329,6 +331,15 @@ if ($OSTYPE =~ /linux/i) {
+     $TOOLS = 'clang' unless ($TOOLS);
+ } elsif ($OSTYPE eq 'win') {
+     $TOOLS = 'vc++';
++} elsif ($OSTYPE =~ /NetBSD/i) {
++    $LPFX = 'lib';
++    $OBJX = 'o';
++    $LOBX = 'pic.o';
++    $LIBX = 'a';
++    $SHLX = 'so';
++    $EXEX = '';
++    $OSINC = 'unix';
++    $TOOLS = 'gcc' unless ($TOOLS);
+ } else {
+     die "unrecognized OS '$OSTYPE'";
+ }
diff --git a/ngs-sdk-all/patches/patch-ngs-python_setup_konfigure.perl b/ngs-sdk-all/patches/patch-ngs-python_setup_konfigure.perl
new file mode 100644
index 0000000000..db3960b913
--- /dev/null
+++ b/ngs-sdk-all/patches/patch-ngs-python_setup_konfigure.perl
@@ -0,0 +1,46 @@
+$NetBSD$
+
+--- ngs-python/setup/konfigure.perl.orig	2015-11-23 18:38:45.000000000 +0000
++++ ngs-python/setup/konfigure.perl
+@@ -198,14 +198,14 @@ print "checking system type... " unless
+ my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
+ println $OSTYPE unless ($AUTORUN);
+ 
+-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'NetBSD') {
+     println "configure: error: unsupported system '$OSTYPE'";
+     exit 1;
+ }
+ 
+ print "checking machine architecture... " unless ($AUTORUN);
+ println $MARCH unless ($AUTORUN);
+-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
++unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /amd64/i) {
+     println "configure: error: unsupported architecture '$OSTYPE'";
+     exit 1;
+ }
+@@ -300,6 +300,8 @@ if ($MARCH =~ /x86_64/i) {
+     $BITS = '32_64';
+ } elsif ($MARCH =~ /i?86/i) {
+     $BITS = 32;
++} elsif ($MARCH =~ /amd64/i) {
++    $BITS = 64;
+ } else {
+     die "unrecognized Architecture '$ARCH'";
+ }
+@@ -329,6 +331,15 @@ if ($OSTYPE =~ /linux/i) {
+     $TOOLS = 'clang' unless ($TOOLS);
+ } elsif ($OSTYPE eq 'win') {
+     $TOOLS = 'vc++';
++} elsif ($OSTYPE =~ /NetBSD/i) {
++    $LPFX = 'lib';
++    $OBJX = 'o';
++    $LOBX = 'pic.o';
++    $LIBX = 'a';
++    $SHLX = 'so';
++    $EXEX = '';
++    $OSINC = 'unix';
++    $TOOLS = 'gcc' unless ($TOOLS);
+ } else {
+     die "unrecognized OS '$OSTYPE'";
+ }
diff --git a/ngs-sdk-all/patches/patch-ngs-sdk_setup_konfigure.perl b/ngs-sdk-all/patches/patch-ngs-sdk_setup_konfigure.perl
new file mode 100644
index 0000000000..5f51feba33
--- /dev/null
+++ b/ngs-sdk-all/patches/patch-ngs-sdk_setup_konfigure.perl
@@ -0,0 +1,46 @@
+$NetBSD$
+
+--- ngs-sdk/setup/konfigure.perl.orig	2015-11-23 18:38:45.000000000 +0000
++++ ngs-sdk/setup/konfigure.perl
+@@ -198,14 +198,14 @@ print "checking system type... " unless
+ my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch();
+ println $OSTYPE unless ($AUTORUN);
+ 
+-unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') {
++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'NetBSD') {
+     println "configure: error: unsupported system '$OSTYPE'";
+     exit 1;
+ }
+ 
+ print "checking machine architecture... " unless ($AUTORUN);
+ println $MARCH unless ($AUTORUN);
+-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) {
++unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /amd64/i) {
+     println "configure: error: unsupported architecture '$OSTYPE'";
+     exit 1;
+ }
+@@ -300,6 +300,8 @@ if ($MARCH =~ /x86_64/i) {
+     $BITS = '32_64';
+ } elsif ($MARCH =~ /i?86/i) {
+     $BITS = 32;
++} elsif ($MARCH =~ /amd64/i) {
++    $BITS = 64;
+ } else {
+     die "unrecognized Architecture '$ARCH'";
+ }
+@@ -329,6 +331,15 @@ if ($OSTYPE =~ /linux/i) {
+     $TOOLS = 'clang' unless ($TOOLS);
+ } elsif ($OSTYPE eq 'win') {
+     $TOOLS = 'vc++';
++} elsif ($OSTYPE =~ /NetBSD/i) {
++    $LPFX = 'lib';
++    $OBJX = 'o';
++    $LOBX = 'pic.o';
++    $LIBX = 'a';
++    $SHLX = 'so';
++    $EXEX = '';
++    $OSINC = 'unix';
++    $TOOLS = 'gcc' unless ($TOOLS);
+ } else {
+     die "unrecognized OS '$OSTYPE'";
+ }