BSD Ports

biology/ngs-sdk 3.0.1 FreeBSD

Tools and libraries for using data in the INSDC Sequence Read Archives

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
PD
Categories
biology

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.

In the other systems

The newest version among them is 3.0.1, as upstream numbers it.

SystemPortVersionVulnerabilitiesStatusMaintainerLast update
FreeBSDbiology/ngs-sdk3.0.1 newestnone known-[email protected]-
DragonFlybiology/ngs-sdk3.0.1 newestnone known-[email protected]-
HardenedBSDbiology/ngs-sdk3.0.1 newestno data-[email protected]-
GhostBSDbiology/ngs-sdk3.0.1 newestno data-[email protected]-

Install

Binary package:

pkg install ngs-sdk

From the ports tree:

cd /usr/ports/biology/ngs-sdk/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	ngs-sdk>0:biology/ngs-sdk
LIB_DEPENDS=	libngs-sdk.so:biology/ngs-sdk

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest-3.0.1--3.0.1
FreeBSD:14:quarterly-3.0.1n/a-3.0.1
FreeBSD:15:latest-3.0.1n/a-3.0.1
FreeBSD:15:quarterly-3.0.1n/an/an/a
FreeBSD:16:latest-3.0.1n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependency graph

Ports that need it on the left, what it needs to run on the right (to build, as it needs nothing to run); at most 8 of each. "Dependencies" below lists them all.

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Build dependencies 4

No port depends on this one.

Configuration

No options to configure.

USES
compiler:c++11-lang gmake perl5
Service scripts
none

Files

pkg-plist 100
  • include/ngs/Alignment.hpp
  • include/ngs/AlignmentIterator.hpp
  • include/ngs/ErrorMsg.hpp
  • include/ngs/Fragment.hpp
  • include/ngs/FragmentIterator.hpp
  • include/ngs/Package.hpp
  • include/ngs/Pileup.hpp
  • include/ngs/PileupEvent.hpp
  • include/ngs/PileupEventIterator.hpp
  • include/ngs/PileupIterator.hpp
  • include/ngs/Read.hpp
  • include/ngs/ReadCollection.hpp
  • include/ngs/ReadGroup.hpp
  • include/ngs/ReadGroupIterator.hpp
  • include/ngs/ReadIterator.hpp
  • include/ngs/Reference.hpp
  • include/ngs/ReferenceIterator.hpp
  • include/ngs/ReferenceSequence.hpp
  • include/ngs/Statistics.hpp
  • include/ngs/StringRef.hpp
  • include/ngs/adapter/AlignmentItf.hpp
  • include/ngs/adapter/ErrorMsg.hpp
  • include/ngs/adapter/FragmentItf.hpp
  • include/ngs/adapter/PileupEventItf.hpp
  • include/ngs/adapter/PileupItf.hpp
  • include/ngs/adapter/ReadCollectionItf.hpp
  • include/ngs/adapter/ReadGroupItf.hpp
  • include/ngs/adapter/ReadItf.hpp
  • include/ngs/adapter/Refcount.hpp
  • include/ngs/adapter/ReferenceItf.hpp
  • include/ngs/adapter/ReferenceSequenceItf.hpp
  • include/ngs/adapter/StatisticsItf.hpp
  • include/ngs/adapter/StringItf.hpp
  • include/ngs/adapter/defs.h
  • include/ngs/inl/Alignment.hpp
  • include/ngs/inl/AlignmentIterator.hpp
  • include/ngs/inl/Fragment.hpp
  • include/ngs/inl/FragmentIterator.hpp
  • include/ngs/inl/Package.hpp
  • include/ngs/inl/Pileup.hpp
  • include/ngs/inl/PileupEvent.hpp
  • include/ngs/inl/PileupEventIterator.hpp
  • include/ngs/inl/PileupIterator.hpp
  • include/ngs/inl/Read.hpp
  • include/ngs/inl/ReadCollection.hpp
  • include/ngs/inl/ReadGroup.hpp
  • include/ngs/inl/ReadGroupIterator.hpp
  • include/ngs/inl/ReadIterator.hpp
  • include/ngs/inl/Reference.hpp
  • include/ngs/inl/ReferenceIterator.hpp
  • include/ngs/inl/ReferenceSequence.hpp
  • include/ngs/inl/Statistics.hpp
  • include/ngs/inl/StringRef.hpp
  • include/ngs/itf/AlignmentItf.h
  • include/ngs/itf/AlignmentItf.hpp
  • include/ngs/itf/ErrBlock.h
  • include/ngs/itf/ErrBlock.hpp
  • include/ngs/itf/ErrorMsg.hpp
  • include/ngs/itf/FragmentItf.h
  • include/ngs/itf/FragmentItf.hpp
  • include/ngs/itf/PackageItf.hpp
  • include/ngs/itf/PileupEventItf.h
  • include/ngs/itf/PileupEventItf.hpp
  • include/ngs/itf/PileupItf.h
  • include/ngs/itf/PileupItf.hpp
  • include/ngs/itf/ReadCollectionItf.h
  • include/ngs/itf/ReadCollectionItf.hpp
  • include/ngs/itf/ReadGroupItf.h
  • include/ngs/itf/ReadGroupItf.hpp
  • include/ngs/itf/ReadItf.h
  • include/ngs/itf/ReadItf.hpp
  • include/ngs/itf/Refcount.h
  • include/ngs/itf/Refcount.hpp
  • include/ngs/itf/ReferenceItf.h
  • include/ngs/itf/ReferenceItf.hpp
  • include/ngs/itf/ReferenceSequenceItf.h
  • include/ngs/itf/ReferenceSequenceItf.hpp
  • include/ngs/itf/StatisticsItf.h
  • include/ngs/itf/StatisticsItf.hpp
  • include/ngs/itf/StringItf.h
  • include/ngs/itf/StringItf.hpp
  • include/ngs/itf/VTable.h
  • include/ngs/itf/VTable.hpp
  • include/ngs/itf/defs.h
  • include/ngs/unix/amd64
  • include/ngs/unix/arm64/atomic32.h
  • include/ngs/unix/fat86/atomic32.h
  • include/ngs/unix/i386/atomic32.h
  • include/ngs/unix/x86_64/atomic32.h
  • lib/libngs-adapt-c++-static.a
  • lib/libngs-adapt-c++.a
  • lib/libngs-adapt-c++.a.2
  • lib/libngs-adapt-c++.a.2.11.2
  • lib/libngs-c++-static.a
  • lib/libngs-c++.a
  • lib/libngs-c++.a.2
  • lib/libngs-c++.a.2.11.2
  • lib/libngs-sdk.so
  • lib/libngs-sdk.so.2
  • lib/libngs-sdk.so.2.11.2
distinfo 1
FileSizeSHA256
ncbi-ngs-3.0.1_GH0.tar.gz1.101663e+060c326aa1744a689c67d2ee7ef8097ec962fdc1529ddbfd63eb0987a23e76d48e

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