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Port details
ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives
3.0.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 3.0.1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-06-10 23:58:19
Last Update: 2024-02-02 21:33:37
Commit Hash: 076c40f
License: PD
WWW:
https://github.com/ncbi/ngs
Description:
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. The API is currently expressed in C++, Java and Python languages. The design makes it possible to maintain a high degree of similarity between the code in one language and code in another - especially between C++ and Java.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (107 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/ngs-sdk-3.0.1/catalog.mk
  3. /usr/local/share/licenses/ngs-sdk-3.0.1/LICENSE
  4. /usr/local/share/licenses/ngs-sdk-3.0.1/PD
  5. include/ngs/Alignment.hpp
  6. include/ngs/AlignmentIterator.hpp
  7. include/ngs/ErrorMsg.hpp
  8. include/ngs/Fragment.hpp
  9. include/ngs/FragmentIterator.hpp
  10. include/ngs/Package.hpp
  11. include/ngs/Pileup.hpp
  12. include/ngs/PileupEvent.hpp
  13. include/ngs/PileupEventIterator.hpp
  14. include/ngs/PileupIterator.hpp
  15. include/ngs/Read.hpp
  16. include/ngs/ReadCollection.hpp
  17. include/ngs/ReadGroup.hpp
  18. include/ngs/ReadGroupIterator.hpp
  19. include/ngs/ReadIterator.hpp
  20. include/ngs/Reference.hpp
  21. include/ngs/ReferenceIterator.hpp
  22. include/ngs/ReferenceSequence.hpp
  23. include/ngs/Statistics.hpp
  24. include/ngs/StringRef.hpp
  25. include/ngs/adapter/AlignmentItf.hpp
  26. include/ngs/adapter/ErrorMsg.hpp
  27. include/ngs/adapter/FragmentItf.hpp
  28. include/ngs/adapter/PileupEventItf.hpp
  29. include/ngs/adapter/PileupItf.hpp
  30. include/ngs/adapter/ReadCollectionItf.hpp
  31. include/ngs/adapter/ReadGroupItf.hpp
  32. include/ngs/adapter/ReadItf.hpp
  33. include/ngs/adapter/Refcount.hpp
  34. include/ngs/adapter/ReferenceItf.hpp
  35. include/ngs/adapter/ReferenceSequenceItf.hpp
  36. include/ngs/adapter/StatisticsItf.hpp
  37. include/ngs/adapter/StringItf.hpp
  38. include/ngs/adapter/defs.h
  39. include/ngs/inl/Alignment.hpp
  40. include/ngs/inl/AlignmentIterator.hpp
  41. include/ngs/inl/Fragment.hpp
  42. include/ngs/inl/FragmentIterator.hpp
  43. include/ngs/inl/Package.hpp
  44. include/ngs/inl/Pileup.hpp
  45. include/ngs/inl/PileupEvent.hpp
  46. include/ngs/inl/PileupEventIterator.hpp
  47. include/ngs/inl/PileupIterator.hpp
  48. include/ngs/inl/Read.hpp
  49. include/ngs/inl/ReadCollection.hpp
  50. include/ngs/inl/ReadGroup.hpp
  51. include/ngs/inl/ReadGroupIterator.hpp
  52. include/ngs/inl/ReadIterator.hpp
  53. include/ngs/inl/Reference.hpp
  54. include/ngs/inl/ReferenceIterator.hpp
  55. include/ngs/inl/ReferenceSequence.hpp
  56. include/ngs/inl/Statistics.hpp
  57. include/ngs/inl/StringRef.hpp
  58. include/ngs/itf/AlignmentItf.h
  59. include/ngs/itf/AlignmentItf.hpp
  60. include/ngs/itf/ErrBlock.h
  61. include/ngs/itf/ErrBlock.hpp
  62. include/ngs/itf/ErrorMsg.hpp
  63. include/ngs/itf/FragmentItf.h
  64. include/ngs/itf/FragmentItf.hpp
  65. include/ngs/itf/PackageItf.hpp
  66. include/ngs/itf/PileupEventItf.h
  67. include/ngs/itf/PileupEventItf.hpp
  68. include/ngs/itf/PileupItf.h
  69. include/ngs/itf/PileupItf.hpp
  70. include/ngs/itf/ReadCollectionItf.h
  71. include/ngs/itf/ReadCollectionItf.hpp
  72. include/ngs/itf/ReadGroupItf.h
  73. include/ngs/itf/ReadGroupItf.hpp
  74. include/ngs/itf/ReadItf.h
  75. include/ngs/itf/ReadItf.hpp
  76. include/ngs/itf/Refcount.h
  77. include/ngs/itf/Refcount.hpp
  78. include/ngs/itf/ReferenceItf.h
  79. include/ngs/itf/ReferenceItf.hpp
  80. include/ngs/itf/ReferenceSequenceItf.h
  81. include/ngs/itf/ReferenceSequenceItf.hpp
  82. include/ngs/itf/StatisticsItf.h
  83. include/ngs/itf/StatisticsItf.hpp
  84. include/ngs/itf/StringItf.h
  85. include/ngs/itf/StringItf.hpp
  86. include/ngs/itf/VTable.h
  87. include/ngs/itf/VTable.hpp
  88. include/ngs/itf/defs.h
  89. include/ngs/unix/amd64
  90. include/ngs/unix/arm64/atomic32.h
  91. include/ngs/unix/fat86/atomic32.h
  92. include/ngs/unix/i386/atomic32.h
  93. include/ngs/unix/x86_64/atomic32.h
  94. lib/libngs-adapt-c++-static.a
  95. lib/libngs-adapt-c++.a
  96. lib/libngs-adapt-c++.a.2
  97. lib/libngs-adapt-c++.a.2.11.2
  98. lib/libngs-c++-static.a
  99. lib/libngs-c++.a
  100. lib/libngs-c++.a.2
  101. lib/libngs-c++.a.2.11.2
  102. lib/libngs-sdk.so
  103. lib/libngs-sdk.so.2
  104. lib/libngs-sdk.so.2.11.2
  105. @owner
  106. @group
  107. @mode
Collapse this list.
Dependency lines:
  • ngs-sdk>0:biology/ngs-sdk
To install the port:
cd /usr/ports/biology/ngs-sdk/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ngs-sdk
  • pkg install ngs-sdk
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ngs-sdk
Flavors: there is no flavor information for this port.
NOT_FOR_ARCHS: powerpc powerpc64 powerpc64le
distinfo:
TIMESTAMP = 1687816957 SHA256 (ncbi-ngs-3.0.1_GH0.tar.gz) = 0c326aa1744a689c67d2ee7ef8097ec962fdc1529ddbfd63eb0987a23e76d48e SIZE (ncbi-ngs-3.0.1_GH0.tar.gz) = 1101663
Packages (timestamps in pop-ups are UTC):
ngs-sdk
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-3.0.1--3.0.1---
FreeBSD:13:quarterly-3.0.1--3.0.1---
FreeBSD:14:latest-3.0.1--3.0.1---
FreeBSD:14:quarterly-3.0.1--3.0.1---
FreeBSD:15:latest-3.0.1n/a-n/a---
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. perl5>=5.36<5.37 : lang/perl5.36
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_ngs-sdk
USES:
compiler:c++11-lang gmake perl5
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/ncbi/ngs/tar.gz/3.0.1?dummy=/
Collapse this list.

Number of commits found: 30

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.0.1
02 Feb 2024 21:33:37
commit hash: 076c40f6357823af28facd2c635ce6a132e0f8f2commit hash: 076c40f6357823af28facd2c635ce6a132e0f8f2commit hash: 076c40f6357823af28facd2c635ce6a132e0f8f2commit hash: 076c40f6357823af28facd2c635ce6a132e0f8f2 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Not for powerpc, powerpc64le
3.0.1
26 Jun 2023 22:51:40
commit hash: 3b489c6e56767a2c6801cc6bdc5694654067feb0commit hash: 3b489c6e56767a2c6801cc6bdc5694654067feb0commit hash: 3b489c6e56767a2c6801cc6bdc5694654067feb0commit hash: 3b489c6e56767a2c6801cc6bdc5694654067feb0 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Update 2.11.2 → 3.0.1

Reported by:	portscout
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.11.2
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.11.2
22 Jul 2022 22:34:07
commit hash: 768fb66f822a80cbc91c7d1f89bb2336db0be121commit hash: 768fb66f822a80cbc91c7d1f89bb2336db0be121commit hash: 768fb66f822a80cbc91c7d1f89bb2336db0be121commit hash: 768fb66f822a80cbc91c7d1f89bb2336db0be121 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Broken on armv6, armv7

Reported by:	fallout
2.11.2
07 Jul 2022 01:33:58
commit hash: d3e958636916e711fa0437b21b617c16f026d64ecommit hash: d3e958636916e711fa0437b21b617c16f026d64ecommit hash: d3e958636916e711fa0437b21b617c16f026d64ecommit hash: d3e958636916e711fa0437b21b617c16f026d64e files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools

This reverts commit 1cb8897f610a381ddf2802eb09acfba97b15b505.

sra-tools needs to be updated first.

Reported by:	Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@
2.11.2
06 Jul 2022 19:03:11
commit hash: 1cb8897f610a381ddf2802eb09acfba97b15b505commit hash: 1cb8897f610a381ddf2802eb09acfba97b15b505commit hash: 1cb8897f610a381ddf2802eb09acfba97b15b505commit hash: 1cb8897f610a381ddf2802eb09acfba97b15b505 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Remove, ngs was moved into sra-tools
2.11.2
27 Jan 2022 09:29:09
commit hash: 3bd735f3aaeefd25d8b4b441e1b109b82fe23d29commit hash: 3bd735f3aaeefd25d8b4b441e1b109b82fe23d29commit hash: 3bd735f3aaeefd25d8b4b441e1b109b82fe23d29commit hash: 3bd735f3aaeefd25d8b4b441e1b109b82fe23d29 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Update 2.11.1 -> 2.11.2

Reported by:	portscout
2.11.1
18 Aug 2021 17:17:44
commit hash: e231650c4aeb1c62fbd6e95ba7354dd07af64a33commit hash: e231650c4aeb1c62fbd6e95ba7354dd07af64a33commit hash: e231650c4aeb1c62fbd6e95ba7354dd07af64a33commit hash: e231650c4aeb1c62fbd6e95ba7354dd07af64a33 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Update 2.11.0-> 2.11.1

Reported by:	portscout
2.11.0_2
15 Apr 2021 17:01:31
commit hash: b2993cf7f634f1cacc48e1557f335926fc3efd93commit hash: b2993cf7f634f1cacc48e1557f335926fc3efd93commit hash: b2993cf7f634f1cacc48e1557f335926fc3efd93commit hash: b2993cf7f634f1cacc48e1557f335926fc3efd93 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by
explicit 'amd64' instead of $ARCH

Reported by:	fallout
2.11.0_2
12 Apr 2021 17:47:50
commit hash: fc2fe6e33a4b7403d4e02aef65440631b4cc55b8commit hash: fc2fe6e33a4b7403d4e02aef65440631b4cc55b8commit hash: fc2fe6e33a4b7403d4e02aef65440631b4cc55b8commit hash: fc2fe6e33a4b7403d4e02aef65440631b4cc55b8 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Restore static libs installed with symlinks as shared libs are
usually installed

Symlinks like this libxx.a->libxx.a.N.N.N first looked broken but it turned out
that this is intentional.
2.11.0_1
12 Apr 2021 08:51:03
commit hash: dd048035a8f50b282d6dc310f19587007eda8fc2commit hash: dd048035a8f50b282d6dc310f19587007eda8fc2commit hash: dd048035a8f50b282d6dc310f19587007eda8fc2commit hash: dd048035a8f50b282d6dc310f19587007eda8fc2 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Improve the 'install' target and other parts of Makefile,
report issues to upstream.
2.11.0
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.11.0
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
Remove # $FreeBSD$ from Makefiles.
2.11.0
20 Mar 2021 06:39:39
Revision:568842Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.9 -> 2.11.0

Reported by:	portscout
2.10.9
02 Jan 2021 01:46:09
Revision:559904Original commit files touched by this commit		 linimon search for other commits by this committer 
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)
2.10.9
17 Dec 2020 20:12:12
Revision:558319Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.5 -> 2.10.9

Reported by:	portscout
2.10.5
04 Apr 2020 20:09:00
Revision:530713Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.4 -> 2.10.5

Reported by:	portscout
2.10.4
07 Mar 2020 19:58:39
Revision:527973Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.2 -> 2.10.4

Reported by:	portscout
2.10.2
17 Jan 2020 07:05:29
Revision:523285Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.1 -> 2.10.2

Reported by:	portscout
2.10.1
12 Jan 2020 02:43:07
Revision:522744Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.0 -> 2.10.1

Reported by:	portscout
2.10.0
31 Aug 2019 15:09:47
Revision:510395Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.6 -> 2.10.0

Reported by:	portscout
2.9.6
25 Jun 2019 12:17:05
Revision:505081Original commit files touched by this commit		 linimon search for other commits by this committer 
Mark this port as not buildable on powerpc64:

  *** File 'Makefile.config.FreeBSD.powerpc' is missing. Please run ./configure

The configuration script may have other problems as well.  This needs
to be addressed by upstream (if there is interest).

Approved by:	portmgr (tier-2 blanket)
2.9.6
31 Mar 2019 03:31:59
Revision:497382Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.4 -> 2.9.6

Reported by:	portscout
2.9.4
23 Feb 2019 21:55:55
Revision:493731Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.3 -> 2.9.4

Reported by:	portscout
2.9.3
18 Oct 2018 21:38:22
Revision:482381Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.2 -> 2.9.3
2.9.2
19 Sep 2018 18:09:37
Revision:480103Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.1 -> 2.9.2

Reported by:	portscout
2.9.1
25 Jun 2018 05:04:46
Revision:473291Original commit files touched by this commit		 linimon search for other commits by this committer 
Mark as broken on aarch64.

Approved by:	portmgr (tier-2 blanket)
2.9.1
22 Jun 2018 09:33:47
Revision:473028Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.0 -> 2.9.1

Reported by:	portscout
2.9.0
10 Jun 2018 23:58:07
Revision:472158Original commit files touched by this commit		 yuri search for other commits by this committer 
New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC
Sequence Read Archives

Number of commits found: 30
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