New Upstream Release - ngs-sdk

Ready changes

Summary

Merged new upstream version: 3.0.1 (was: 2.11.2).

Resulting package

Built on 2022-12-14T20:41 (took 6m38s)

The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:

apt install -t fresh-releases libngs-javaapt install -t fresh-releases libngs-sdk-devapt install -t fresh-releases libngs-sdk2-dbgsymapt install -t fresh-releases libngs-sdk2apt install -t fresh-releases python3-ngs

Diff

diff --git a/CHANGES.md b/CHANGES.md
index d4267fa..987242a 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,5 +1,16 @@
 # NCBI External Developer Release:
 
+### NGS SDK 3.0.1
+**November 15, 2022**
+
+  SRA tolkit release 3.0.1.
+
+
+### NGS SDK 3.0.0
+**February 10, 2022**
+
+  **ngs**: https://github.com/ncbi/ngs repository is now frozen. The NGS project has moved to https://github.com/ncbi/sra-tools/ngs.
+
 
 ## NGS SDK 2.11.2
 **October 7, 2021**
diff --git a/README.md b/README.md
index cb19a24..f86d0b8 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,44 @@
 ngs
 ===
 
+## ANNOUNCEMENTS:
+
+### This repository is now frozen. The NGS project has moved to https://github.com/ncbi/sra-tools/ngs. See the full announcement below.
+
+February 10, 2022
+
+NCBI's SRA changed the source build system to use CMake in toolkit release 3.0.0. This change is an important step to improve developers' productivity as it provides unified cross platform access to support multiple build systems. This change affects developers building NCBI SRA tools from source. Old makefiles and build systems are no longer supported.
+
+This change also includes the structure of GitHub repositories, which underwent consolidation to provide an easier environment for building tools and libraries (NGS libs and dependencies are consolidated). Consolidation of NGS libraries and dependencies provides better usage scope isolation and makes building more straightforward.
+
+#### **Affected repositories**
+
+1) [ncbi/ngs](https://github.com/ncbi/ngs) (This repository)
+
+   This repository is frozen. All future development will take place in GitHub repository ncbi/sra-tools (this repository), under subdirectory `ngs/`.
+
+2) [ncbi/ncbi-vdb](https://github.com/ncbi/ncbi-vdb)
+
+   This project's build system is based on CMake. The libraries providing access to SRA data in VDB format via the NGS API have moved to GitHub repository
+   [ncbi/sra-tools](https://github.com/ncbi/ncbi-vdb).
+
+   | Old (base URL: https://github.com/ncbi/ncbi-vdb) | New (base URL: https://github.com/ncbi/sra-tools) |
+   | -------------------------------------------------| ------------------------------------------------- |
+   | `libs/ngs`        | `ngs/ncbi/ngs`     |
+   | `libs/ngs-c++`    | `ngs/ncbi/ngs-c++` |
+   | `libs/ngs-jni`    | `ngs/ncbi/ngs-jni` |
+   | `libs/ngs-py`     | `ngs/ncbi/ngs-py`  |
+   | `libs/vdb-sqlite` | `libs/vdb-sqlite`  |
+   | `test/ngs-java`   | `test/ngs-java`    |
+   | `test/ngs-python` | `test/ngs-python`  |
+
+
+3) [ncbi/sra-tools](https://github.com/ncbi/sra-tools)
+
+   This project's build system is based on CMake. The project acquired some new components, as listed in the table above.
+
+----
+
 # NGS Language Bindings
 
 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. The API itself is independent from any particular back-end implementation, and supports use of multiple back-ends simultaneously. It also provides a library for building new back-end "engines". The engine for accessing SRA data is contained within the sister repository [ncbi-vdb](https://github.com/ncbi/ncbi-vdb).
diff --git a/debian/changelog b/debian/changelog
index fc57688..5943651 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+ngs-sdk (3.0.1-1) UNRELEASED; urgency=low
+
+  * New upstream release.
+
+ -- Debian Janitor <janitor@jelmer.uk>  Wed, 14 Dec 2022 20:36:19 -0000
+
 ngs-sdk (2.11.2-4) unstable; urgency=medium
 
   * Team upload
diff --git a/debian/patches/do_not_exclude_certain_architectures_explicitly.patch b/debian/patches/do_not_exclude_certain_architectures_explicitly.patch
index 2ace7a0..ccc70b6 100644
--- a/debian/patches/do_not_exclude_certain_architectures_explicitly.patch
+++ b/debian/patches/do_not_exclude_certain_architectures_explicitly.patch
@@ -4,8 +4,10 @@ Bug-Debian: https://bugs.debian.org/813559
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Wed, 03 Feb 2016 07:53:29 +0100
 
---- a/ngs-bam/setup/konfigure.perl
-+++ b/ngs-bam/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-bam/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-bam/setup/konfigure.perl
++++ ngs-sdk.git/ngs-bam/setup/konfigure.perl
 @@ -226,8 +226,7 @@ if ($OS eq 'linux') {
  print "checking machine architecture... " unless ($AUTORUN);
  println $MARCH unless ($AUTORUN);
@@ -16,8 +18,10 @@ Last-Update: Wed, 03 Feb 2016 07:53:29 +0100
  }
  
  {
---- a/ngs-java/setup/konfigure.perl
-+++ b/ngs-java/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-java/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-java/setup/konfigure.perl
++++ ngs-sdk.git/ngs-java/setup/konfigure.perl
 @@ -226,8 +226,7 @@ if ($OS eq 'linux') {
  print "checking machine architecture... " unless ($AUTORUN);
  println $MARCH unless ($AUTORUN);
@@ -28,8 +32,10 @@ Last-Update: Wed, 03 Feb 2016 07:53:29 +0100
  }
  
  {
---- a/ngs-python/setup/konfigure.perl
-+++ b/ngs-python/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-python/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-python/setup/konfigure.perl
++++ ngs-sdk.git/ngs-python/setup/konfigure.perl
 @@ -226,8 +226,7 @@ if ($OS eq 'linux') {
  print "checking machine architecture... " unless ($AUTORUN);
  println $MARCH unless ($AUTORUN);
@@ -40,8 +46,10 @@ Last-Update: Wed, 03 Feb 2016 07:53:29 +0100
  }
  
  {
---- a/ngs-sdk/setup/konfigure.perl
-+++ b/ngs-sdk/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-sdk/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/setup/konfigure.perl
++++ ngs-sdk.git/ngs-sdk/setup/konfigure.perl
 @@ -226,8 +226,7 @@ if ($OS eq 'linux') {
  print "checking machine architecture... " unless ($AUTORUN);
  println $MARCH unless ($AUTORUN);
diff --git a/debian/patches/enable-ppc64el.patch b/debian/patches/enable-ppc64el.patch
index 8f4fb25..c5522be 100644
--- a/debian/patches/enable-ppc64el.patch
+++ b/debian/patches/enable-ppc64el.patch
@@ -1,8 +1,10 @@
 Description: Enable ppc64 and ppc64el
 Handle those architectures in the configuration scripts.
 Author: Frédéric Bonnard <frediz@debian.org>
---- a/ngs-bam/setup/os-arch.prl
-+++ b/ngs-bam/setup/os-arch.prl
+Index: ngs-sdk.git/ngs-bam/setup/os-arch.prl
+===================================================================
+--- ngs-sdk.git.orig/ngs-bam/setup/os-arch.prl
++++ ngs-sdk.git/ngs-bam/setup/os-arch.prl
 @@ -55,6 +55,9 @@ sub OsArch {
              } elsif ($MARCH =~ /sun4v/) {
                  $HOST_ARCH = 'sparc64';
@@ -13,8 +15,10 @@ Author: Frédéric Bonnard <frediz@debian.org>
              } elsif ($MARCH =~ /aarch64/) {
                  $HOST_ARCH = 'arm64';
              } else {
---- a/ngs-java/setup/os-arch.prl
-+++ b/ngs-java/setup/os-arch.prl
+Index: ngs-sdk.git/ngs-java/setup/os-arch.prl
+===================================================================
+--- ngs-sdk.git.orig/ngs-java/setup/os-arch.prl
++++ ngs-sdk.git/ngs-java/setup/os-arch.prl
 @@ -55,6 +55,9 @@ sub OsArch {
              } elsif ($MARCH =~ /sun4v/) {
                  $HOST_ARCH = 'sparc64';
@@ -25,8 +29,10 @@ Author: Frédéric Bonnard <frediz@debian.org>
              } elsif ($MARCH =~ /aarch64/) {
                  $HOST_ARCH = 'arm64';
              } else {
---- a/ngs-python/setup/os-arch.prl
-+++ b/ngs-python/setup/os-arch.prl
+Index: ngs-sdk.git/ngs-python/setup/os-arch.prl
+===================================================================
+--- ngs-sdk.git.orig/ngs-python/setup/os-arch.prl
++++ ngs-sdk.git/ngs-python/setup/os-arch.prl
 @@ -55,6 +55,9 @@ sub OsArch {
              } elsif ($MARCH =~ /sun4v/) {
                  $HOST_ARCH = 'sparc64';
@@ -37,8 +43,10 @@ Author: Frédéric Bonnard <frediz@debian.org>
              } elsif ($MARCH =~ /aarch64/) {
                  $HOST_ARCH = 'arm64';
              } else {
---- a/ngs-sdk/setup/os-arch.prl
-+++ b/ngs-sdk/setup/os-arch.prl
+Index: ngs-sdk.git/ngs-sdk/setup/os-arch.prl
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/setup/os-arch.prl
++++ ngs-sdk.git/ngs-sdk/setup/os-arch.prl
 @@ -55,6 +55,9 @@ sub OsArch {
              } elsif ($MARCH =~ /sun4v/) {
                  $HOST_ARCH = 'sparc64';
diff --git a/debian/patches/fallback-on-generic-atomic32.patch b/debian/patches/fallback-on-generic-atomic32.patch
index d59a2b5..55e534a 100644
--- a/debian/patches/fallback-on-generic-atomic32.patch
+++ b/debian/patches/fallback-on-generic-atomic32.patch
@@ -1,8 +1,10 @@
 Description: Fallback on generic atomic32.h
 Author: Frédéric Bonnard <frediz@debian.org>
 Bug-Debian: https://bugs.debian.org/813559
---- a/ngs-sdk/setup/konfigure.perl
-+++ b/ngs-sdk/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-sdk/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/setup/konfigure.perl
++++ ngs-sdk.git/ngs-sdk/setup/konfigure.perl
 @@ -957,8 +957,13 @@ EndText
      }
      if ($PIC) {
diff --git a/debian/patches/fix_jni.patch b/debian/patches/fix_jni.patch
index 43b9125..5010c2a 100644
--- a/debian/patches/fix_jni.patch
+++ b/debian/patches/fix_jni.patch
@@ -3,8 +3,10 @@ Description: software embeds some jni code, use code from Debian
 Author: Olivier Sallou <osallou@debian.org>
 Last-Updated: 02/01/2016
 Forwarded: no
---- a/ngs-sdk/language/java/jni.h
-+++ b/ngs-sdk/language/java/jni.h
+Index: ngs-sdk.git/ngs-sdk/language/java/jni.h
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/language/java/jni.h
++++ ngs-sdk.git/ngs-sdk/language/java/jni.h
 @@ -24,7 +24,7 @@
  /* jni_md.h contains the machine-dependent typedefs for jbyte, jint
     and jlong */
@@ -14,8 +16,10 @@ Forwarded: no
  
  #ifdef __cplusplus
  extern "C" {
---- a/ngs-sdk/language/java/jni_ErrorMsg.hpp
-+++ b/ngs-sdk/language/java/jni_ErrorMsg.hpp
+Index: ngs-sdk.git/ngs-sdk/language/java/jni_ErrorMsg.hpp
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/language/java/jni_ErrorMsg.hpp
++++ ngs-sdk.git/ngs-sdk/language/java/jni_ErrorMsg.hpp
 @@ -31,7 +31,7 @@
  #include <ngs/itf/ErrBlock.h>
  #endif
@@ -25,8 +29,10 @@ Forwarded: no
  
  
  /*--------------------------------------------------------------------------
---- a/ngs-sdk/language/java/jni_String.hpp
-+++ b/ngs-sdk/language/java/jni_String.hpp
+Index: ngs-sdk.git/ngs-sdk/language/java/jni_String.hpp
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/language/java/jni_String.hpp
++++ ngs-sdk.git/ngs-sdk/language/java/jni_String.hpp
 @@ -31,7 +31,7 @@
  #include <ngs/itf/defs.h>
  #endif
diff --git a/debian/patches/more_archs b/debian/patches/more_archs
index 8a600fb..9964f27 100644
--- a/debian/patches/more_archs
+++ b/debian/patches/more_archs
@@ -1,7 +1,9 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Enable building on more architectures
---- a/ngs-java/setup/konfigure.perl
-+++ b/ngs-java/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-java/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-java/setup/konfigure.perl
++++ ngs-sdk.git/ngs-java/setup/konfigure.perl
 @@ -309,17 +309,7 @@ print "checking for supported architectu
  
  my $BITS;
@@ -21,8 +23,10 @@ Subject: Enable building on more architectures
  println "$MARCH ($BITS bits) is supported" unless ($AUTORUN);
  
  # determine OS and related norms
---- a/ngs-bam/setup/konfigure.perl
-+++ b/ngs-bam/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-bam/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-bam/setup/konfigure.perl
++++ ngs-sdk.git/ngs-bam/setup/konfigure.perl
 @@ -309,17 +309,7 @@ print "checking for supported architectu
  
  my $BITS;
@@ -42,8 +46,10 @@ Subject: Enable building on more architectures
  println "$MARCH ($BITS bits) is supported" unless ($AUTORUN);
  
  # determine OS and related norms
---- a/ngs-python/setup/konfigure.perl
-+++ b/ngs-python/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-python/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-python/setup/konfigure.perl
++++ ngs-sdk.git/ngs-python/setup/konfigure.perl
 @@ -309,17 +309,7 @@ print "checking for supported architectu
  
  my $BITS;
@@ -63,8 +69,10 @@ Subject: Enable building on more architectures
  println "$MARCH ($BITS bits) is supported" unless ($AUTORUN);
  
  # determine OS and related norms
---- a/ngs-sdk/setup/konfigure.perl
-+++ b/ngs-sdk/setup/konfigure.perl
+Index: ngs-sdk.git/ngs-sdk/setup/konfigure.perl
+===================================================================
+--- ngs-sdk.git.orig/ngs-sdk/setup/konfigure.perl
++++ ngs-sdk.git/ngs-sdk/setup/konfigure.perl
 @@ -309,17 +309,7 @@ print "checking for supported architectu
  
  my $BITS;

Debdiff

[The following lists of changes regard files as different if they have different names, permissions or owners.]

Files in second set of .debs but not in first

-rw-r--r--  root/root   /usr/lib/debug/.build-id/39/918e762fa9cc4ed7358af074e26460938c259e.debug
-rw-r--r--  root/root   /usr/share/java/ngs-java-3.0.1.jar
lrwxrwxrwx  root/root   /usr/share/java/ngs-java.jar -> ngs-java-3.0.1.jar

Files in first set of .debs but not in second

-rw-r--r--  root/root   /usr/lib/debug/.build-id/11/57c1217b9afe9449d0bbb9b332e3c2f2a43874.debug
-rw-r--r--  root/root   /usr/share/java/ngs-java-2.11.2.jar
lrwxrwxrwx  root/root   /usr/share/java/ngs-java.jar -> ngs-java-2.11.2.jar

No differences were encountered between the control files of package libngs-java

No differences were encountered between the control files of package libngs-sdk-dev

No differences were encountered between the control files of package libngs-sdk2

Control files of package libngs-sdk2-dbgsym: lines which differ (wdiff format)

  • Build-Ids: 1157c1217b9afe9449d0bbb9b332e3c2f2a43874 39918e762fa9cc4ed7358af074e26460938c259e

No differences were encountered between the control files of package python3-ngs

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