BSD Ports

biology/sra-tools 3.4.1_3 FreeBSD

NCBI's toolkit for handling data in INSDC Sequence Read Archives

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
PD, LGPL21+
Categories
biology, java
Package size
13279.2 KiB, 184601.5 KiB installed

Description

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC (International Nucleotide Sequence Database Collaboration) SRA (Sequence Read Archives). The SRA house sequence reads and alignments generated by DNA/RNA sequencers. The SRA Toolkit facilitates downloading sequence data, performing filtering and conversions on-the-fly, thus saving enormous amounts of time, bandwidth, and storage.

In the other systems

SystemPortVersion
FreeBSDbiology/sra-tools3.4.1_3
NetBSDbiology/sra-tools3.2.0nb2
DragonFlybiology/sra-tools2.11.0_4
HardenedBSDbiology/sra-tools3.4.1_3
GhostBSDbiology/sra-tools3.4.1_3

Install

Binary package:

pkg install sra-tools

From the ports tree:

cd /usr/ports/biology/sra-tools/ && make install clean

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

RUN_DEPENDS=	sra-tools>0:biology/sra-tools
LIB_DEPENDS=	libncbi-ngs.so:biology/sra-tools

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:latest3.4.1_33.4.1_3---
FreeBSD:14:quarterly3.4.1_33.4.1_3n/a--
FreeBSD:15:latest3.4.1_33.4.1_3n/a--
FreeBSD:15:quarterly3.4.1_33.4.1_3n/an/an/a
FreeBSD:16:latest3.4.1_33.4.1_3n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Runtime 1

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

Build dependencies 65
Run dependencies 60

Configuration

Options name: biology_sra-tools

OptionDefaultDescription
EXAMPLESoffBuild and/or install examples
USES
bison cmake java shebangfix
Service scripts
none

Message after installing

===>   NOTICE:

The sra-tools port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

pkg-plist 228
  • bin/abi-dump
  • bin/abi-dump.3
  • bin/abi-dump.
  • bin/align-info
  • bin/align-info.3
  • bin/align-info.
  • bin/check-corrupt
  • bin/check-corrupt.3
  • bin/check-corrupt.
  • bin/fasterq-dump
  • bin/fasterq-dump-orig.
  • bin/fasterq-dump.3
  • bin/fasterq-dump.
  • bin/fastq-dump
  • bin/fastq-dump-orig.
  • bin/fastq-dump.3
  • bin/fastq-dump.
  • bin/illumina-dump
  • bin/illumina-dump.3
  • bin/illumina-dump.
  • bin/kdbmeta
  • bin/kdbmeta.3
  • bin/kdbmeta.
  • bin/ngs-pileup
  • bin/ngs-pileup.3
  • bin/ngs-pileup.
  • bin/prefetch
  • bin/prefetch-orig.
  • bin/prefetch.3
  • bin/prefetch.
  • bin/rcexplain
  • bin/rcexplain.3
  • bin/rcexplain.
  • bin/ref-variation
  • bin/ref-variation.3
  • bin/ref-variation.
  • bin/sam-dump
  • bin/sam-dump-orig.
  • bin/sam-dump.3
  • bin/sam-dump.
  • bin/sff-dump
  • bin/sff-dump.3
  • bin/sff-dump.
  • bin/sra-info
  • bin/sra-info.3
  • bin/sra-info.
  • bin/sra-pileup
  • bin/sra-pileup-orig.
  • bin/sra-pileup.3
  • bin/sra-pileup.
  • bin/sra-search
  • bin/sra-search.3
  • bin/sra-search.
  • bin/sra-stat
  • bin/sra-stat.3
  • bin/sra-stat.
  • bin/srapath
  • bin/srapath-orig.
  • bin/srapath.3
  • bin/srapath.
  • bin/sratools
  • bin/sratools.3
  • bin/sratools.
  • bin/test-sra
  • bin/test-sra.3
  • bin/test-sra.
  • bin/var-expand
  • bin/var-expand.3
  • bin/var-expand.
  • bin/vdb-config
  • bin/vdb-config.3
  • bin/vdb-config.
  • bin/vdb-decrypt
  • bin/vdb-decrypt.3
  • bin/vdb-decrypt.
  • bin/vdb-dump
  • bin/vdb-dump-orig.
  • bin/vdb-dump.3
  • bin/vdb-dump.
  • bin/vdb-encrypt
  • bin/vdb-encrypt.3
  • bin/vdb-encrypt.
  • bin/vdb-validate
  • bin/vdb-validate.3
  • bin/vdb-validate.
  • include/ncbi-vdb/NGS.hpp
  • 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

The first 100 are listed.

distinfo 2
FileSizeSHA256
ncbi-sra-tools-3.4.1_GH0.tar.gz6.6796004e+07874dcbb28b7ebffb5554839254e777b1137b0f0430815bab175068decfe96e98
ncbi-ncbi-vdb-3.4.1_GH0.tar.gz1.9106888e+072fa0919b2842641ead93eeeb45047e87ca480a543b6e4eda15f94d5187e91c85

Commit history 1

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.