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Port details
ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives
2.11.2 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 Version 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: 2022-07-22 22:34:07
Commit Hash: 768fb66
License: PD
Description:
SVNWeb : git : Homepage
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-2.11.2/catalog.mk
  3. /usr/local/share/licenses/ngs-sdk-2.11.2/LICENSE
  4. /usr/local/share/licenses/ngs-sdk-2.11.2/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: powerpc64
distinfo:
Packages (timestamps in pop-ups are UTC):
ngs-sdk
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.11.12.11.0_2
FreeBSD:11:armv6--
FreeBSD:11:i3862.11.12.11.0_2
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd642.11.22.11.2
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3862.11.22.11.2
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd642.11.22.11.2
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3862.11.22.11.2
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:13:riscv64--
FreeBSD:14:aarch64--
FreeBSD:14:amd642.11.2-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862.11.2-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
FreeBSD:14:riscv64--
 
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>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Build
  1. biology/sra-tools
Configuration Options:
Options name:
USES:
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/2.11.2?dummy=/
Collapse this list.

Number of commits found: 26

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
22 Jul 2022 22:34:07
 files touched by this commit commit hash:768fb66f822a80cbc91c7d1f89bb2336db0be121  2.11.2		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Broken on armv6, armv7

Reported by:	fallout
07 Jul 2022 01:33:58
 files touched by this commit commit hash:d3e958636916e711fa0437b21b617c16f026d64e  2.11.2		 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@
06 Jul 2022 19:03:11
 files touched by this commit commit hash:1cb8897f610a381ddf2802eb09acfba97b15b505  2.11.2		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Remove, ngs was moved into sra-tools
27 Jan 2022 09:29:09
 files touched by this commit commit hash:3bd735f3aaeefd25d8b4b441e1b109b82fe23d29  2.11.2		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/ngs-sdk: Update 2.11.1 -> 2.11.2

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

Reported by:	portscout
15 Apr 2021 17:01:31
 files touched by this commit commit hash:b2993cf7f634f1cacc48e1557f335926fc3efd93  2.11.0_2		 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
12 Apr 2021 17:47:50
 files touched by this commit commit hash:fc2fe6e33a4b7403d4e02aef65440631b4cc55b8  2.11.0_2		 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.
12 Apr 2021 08:51:03
 files touched by this commit commit hash:dd048035a8f50b282d6dc310f19587007eda8fc2  2.11.0_1		 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.
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.11.0		 Mathieu Arnold (mat) search for other commits by this committer 
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.11.0		 Mathieu Arnold (mat) search for other commits by this committer 
Remove # $FreeBSD$ from Makefiles.
20 Mar 2021 06:39:39
Original commit files touched by this commit Revision:568842  2.11.0		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.9 -> 2.11.0

Reported by:	portscout
02 Jan 2021 01:46:09
Original commit files touched by this commit Revision:559904  2.10.9		 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)
17 Dec 2020 20:12:12
Original commit files touched by this commit Revision:558319  2.10.9		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.10.5 -> 2.10.9

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

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

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

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

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

Reported by:	portscout
25 Jun 2019 12:17:05
Original commit files touched by this commit Revision:505081  2.9.6		 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)
31 Mar 2019 03:31:59
Original commit files touched by this commit Revision:497382  2.9.6		 yuri search for other commits by this committer 
biology/ngs-sdk: Update 2.9.4 -> 2.9.6

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

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

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

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

Reported by:	portscout
10 Jun 2018 23:58:07
Original commit files touched by this commit Revision:472158  2.9.0		 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: 26
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