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Port details
ngs-sdk Tools and libraries for using data in the INSDC Sequence Read Archives
2.9.6 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
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-06-10 23:58:19
Last Update: 2019-03-31 04:31:59
SVN Revision: 497382
License: PD
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.

WWW: https://github.com/ncbi/ngs
SVNWeb : Homepage
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (100 items)
  1. /usr/local/share/licenses/ngs-sdk-2.9.6/catalog.mk
  2. /usr/local/share/licenses/ngs-sdk-2.9.6/LICENSE
  3. /usr/local/share/licenses/ngs-sdk-2.9.6/PD
  4. include/ngs/Alignment.hpp
  5. include/ngs/AlignmentIterator.hpp
  6. include/ngs/ErrorMsg.hpp
  7. include/ngs/Fragment.hpp
  8. include/ngs/FragmentIterator.hpp
  9. include/ngs/Package.hpp
  10. include/ngs/Pileup.hpp
  11. include/ngs/PileupEvent.hpp
  12. include/ngs/PileupEventIterator.hpp
  13. include/ngs/PileupIterator.hpp
  14. include/ngs/Read.hpp
  15. include/ngs/ReadCollection.hpp
  16. include/ngs/ReadGroup.hpp
  17. include/ngs/ReadGroupIterator.hpp
  18. include/ngs/ReadIterator.hpp
  19. include/ngs/Reference.hpp
  20. include/ngs/ReferenceIterator.hpp
  21. include/ngs/ReferenceSequence.hpp
  22. include/ngs/Statistics.hpp
  23. include/ngs/StringRef.hpp
  24. include/ngs/adapter/AlignmentItf.hpp
  25. include/ngs/adapter/ErrorMsg.hpp
  26. include/ngs/adapter/FragmentItf.hpp
  27. include/ngs/adapter/PileupEventItf.hpp
  28. include/ngs/adapter/PileupItf.hpp
  29. include/ngs/adapter/ReadCollectionItf.hpp
  30. include/ngs/adapter/ReadGroupItf.hpp
  31. include/ngs/adapter/ReadItf.hpp
  32. include/ngs/adapter/Refcount.hpp
  33. include/ngs/adapter/ReferenceItf.hpp
  34. include/ngs/adapter/ReferenceSequenceItf.hpp
  35. include/ngs/adapter/StatisticsItf.hpp
  36. include/ngs/adapter/StringItf.hpp
  37. include/ngs/adapter/defs.h
  38. include/ngs/inl/Alignment.hpp
  39. include/ngs/inl/AlignmentIterator.hpp
  40. include/ngs/inl/Fragment.hpp
  41. include/ngs/inl/FragmentIterator.hpp
  42. include/ngs/inl/Package.hpp
  43. include/ngs/inl/Pileup.hpp
  44. include/ngs/inl/PileupEvent.hpp
  45. include/ngs/inl/PileupEventIterator.hpp
  46. include/ngs/inl/PileupIterator.hpp
  47. include/ngs/inl/Read.hpp
  48. include/ngs/inl/ReadCollection.hpp
  49. include/ngs/inl/ReadGroup.hpp
  50. include/ngs/inl/ReadGroupIterator.hpp
  51. include/ngs/inl/ReadIterator.hpp
  52. include/ngs/inl/Reference.hpp
  53. include/ngs/inl/ReferenceIterator.hpp
  54. include/ngs/inl/ReferenceSequence.hpp
  55. include/ngs/inl/Statistics.hpp
  56. include/ngs/inl/StringRef.hpp
  57. include/ngs/itf/AlignmentItf.h
  58. include/ngs/itf/AlignmentItf.hpp
  59. include/ngs/itf/ErrBlock.h
  60. include/ngs/itf/ErrBlock.hpp
  61. include/ngs/itf/ErrorMsg.hpp
  62. include/ngs/itf/FragmentItf.h
  63. include/ngs/itf/FragmentItf.hpp
  64. include/ngs/itf/PackageItf.hpp
  65. include/ngs/itf/PileupEventItf.h
  66. include/ngs/itf/PileupEventItf.hpp
  67. include/ngs/itf/PileupItf.h
  68. include/ngs/itf/PileupItf.hpp
  69. include/ngs/itf/ReadCollectionItf.h
  70. include/ngs/itf/ReadCollectionItf.hpp
  71. include/ngs/itf/ReadGroupItf.h
  72. include/ngs/itf/ReadGroupItf.hpp
  73. include/ngs/itf/ReadItf.h
  74. include/ngs/itf/ReadItf.hpp
  75. include/ngs/itf/Refcount.h
  76. include/ngs/itf/Refcount.hpp
  77. include/ngs/itf/ReferenceItf.h
  78. include/ngs/itf/ReferenceItf.hpp
  79. include/ngs/itf/ReferenceSequenceItf.h
  80. include/ngs/itf/ReferenceSequenceItf.hpp
  81. include/ngs/itf/StatisticsItf.h
  82. include/ngs/itf/StatisticsItf.hpp
  83. include/ngs/itf/StringItf.h
  84. include/ngs/itf/StringItf.hpp
  85. include/ngs/itf/VTable.h
  86. include/ngs/itf/VTable.hpp
  87. include/ngs/itf/defs.h
  88. include/ngs/unix/amd64
  89. include/ngs/unix/fat86/atomic32.h
  90. include/ngs/unix/i386/atomic32.h
  91. include/ngs/unix/x86_64/atomic32.h
  92. include/ngs/win/atomic32.h
  93. include/ngs/win/stdbool.h
  94. lib/libngs-adapt-c++.a
  95. lib/libngs-c++.a
  96. lib/libngs-sdk.so
  97. lib/libngs-sdk.so.2
  98. lib/libngs-sdk.so.2.9.6
  99. @postexec /usr/sbin/service ldconfig restart > /dev/null
  100. @postunexec /usr/sbin/service ldconfig restart > /dev/null
  101. 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: pkg install ngs-sdk

PKGNAME: ngs-sdk

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1554002979
SHA256 (ncbi-ngs-2.9.6_GH0.tar.gz) = 4be42f4d62b2376dc2fc4cd992822525bd99f8e1193008c2dab387a2f291405b
SIZE (ncbi-ngs-2.9.6_GH0.tar.gz) = 1092167


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake
  2. perl5>=5.28.r1<5.29 : lang/perl5.28
Runtime dependencies:
  1. perl5>=5.28.r1<5.29 : lang/perl5.28
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
gmake perl5

Master Sites:
  1. https://codeload.github.com/ncbi/ngs/tar.gz/2.9.6?dummy=/

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
31 Mar 2019 03:31:59
Original commit files touched by this commit  2.9.6
Revision:497382
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  2.9.4
Revision:493731
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  2.9.3
Revision:482381
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  2.9.2
Revision:480103
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  2.9.1
Revision:473291
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  2.9.1
Revision:473028
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  2.9.0
Revision:472158
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: 7

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