sra-toolkit_2.3.5-2+dfsg-1ubuntu1_amd64.deb


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Description

sra-toolkit - utilities for the NCBI Sequence Read Archive

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe amd64
Package name sra-toolkit
Package version 2.3.5
Package release 2+dfsg-1ubuntu1
Package architecture amd64
Package type deb
Installed size 4.74 KB
Download size 893.45 KB
Official Mirror archive.ubuntu.com
Tools for reading the SRA archive, generally by converting individual runs
into some commonly used format such as fastq.
The textual dumpers "sra-dump" and "vdb-dump" are provided in this
release as an aid in visual inspection. It is likely that their
actual output formatting will be changed in the near future to a
stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON
THE OUTPUT FORMAT SEEN IN THIS RELEASE.
The "help" information will be improved in near future releases, and
the tool options will become standardized across the set. More documentation
will also be provided documentation on the NCBI web site.
Tool options may change in the next release. Version 1 tool options
will remain supported wherever possible in order to preserve
operation of any existing scripts.

Alternatives

Package Version Architecture Repository
sra-toolkit_2.3.5-2+dfsg-1ubuntu1_i386.deb 2.3.5 i386 Ubuntu Universe
sra-toolkit - - -

Requires

Name Value
libc6 >= 2.14
sra-toolkit-libs0 -
zlib1g >= 1:1.1.4

Download

Type URL
Binary Package sra-toolkit_2.3.5-2+dfsg-1ubuntu1_amd64.deb
Source Package sra-sdk

Install Howto

  1. Update the package index:
    # sudo apt-get update
  2. Install sra-toolkit deb package:
    # sudo apt-get install sra-toolkit

Files

Path
/etc/ncbi/default.kfg
/etc/ncbi/vdb-copy.kfg
/usr/bin/abi-dump
/usr/bin/abi-dump.2
/usr/bin/abi-dump.2.3.5
/usr/bin/abi-load
/usr/bin/abi-load.2
/usr/bin/abi-load.2.3.5
/usr/bin/align-info
/usr/bin/align-info.2
/usr/bin/align-info.2.3.5
/usr/bin/bam-load
/usr/bin/bam-load.2
/usr/bin/bam-load.2.3.5
/usr/bin/cache-mgr
/usr/bin/cache-mgr.2
/usr/bin/cache-mgr.2.3.5
/usr/bin/fastq-dump
/usr/bin/fastq-dump.2
/usr/bin/fastq-dump.2.3.5
/usr/bin/fastq-load
/usr/bin/fastq-load.2
/usr/bin/fastq-load.2.3.5
/usr/bin/helicos-load
/usr/bin/helicos-load.2
/usr/bin/helicos-load.2.3.5
/usr/bin/illumina-dump
/usr/bin/illumina-dump.2
/usr/bin/illumina-dump.2.3.5
/usr/bin/illumina-load
/usr/bin/illumina-load.2
/usr/bin/illumina-load.2.3.5
/usr/bin/kar
/usr/bin/kar.2
/usr/bin/kar.2.3.5
/usr/bin/kdbmeta
/usr/bin/kdbmeta.2
/usr/bin/kdbmeta.2.3.5
/usr/bin/latf-load
/usr/bin/latf-load.2
/usr/bin/latf-load.2.3.5
/usr/bin/nenctool
/usr/bin/nenctool.2
/usr/bin/nenctool.2.3.5
/usr/bin/nencvalid
/usr/bin/nencvalid.2
/usr/bin/nencvalid.2.3.5
/usr/bin/prefetch
/usr/bin/prefetch.2
/usr/bin/prefetch.2.3.5
/usr/bin/rcexplain
/usr/bin/rcexplain.2
/usr/bin/rcexplain.2.3.5
/usr/bin/sam-dump
/usr/bin/sam-dump.2
/usr/bin/sam-dump.2.3.5
/usr/bin/sff-dump
/usr/bin/sff-dump.2
/usr/bin/sff-dump.2.3.5
/usr/bin/sff-load
/usr/bin/sff-load.2
/usr/bin/sff-load.2.3.5
/usr/bin/sra-kar
/usr/bin/sra-kar.2
/usr/bin/sra-kar.2.3.5
/usr/bin/sra-pileup
/usr/bin/sra-pileup.2
/usr/bin/sra-pileup.2.3.5
/usr/bin/sra-sort
/usr/bin/sra-sort.2
/usr/bin/sra-sort.2.3.5
/usr/bin/sra-stat
/usr/bin/sra-stat.2
/usr/bin/sra-stat.2.3.5
/usr/bin/srapath
/usr/bin/srapath.2
/usr/bin/srapath.2.3.5
/usr/bin/srf-load
/usr/bin/srf-load.2
/usr/bin/srf-load.2.3.5
/usr/bin/test-sra
/usr/bin/test-sra.2
/usr/bin/test-sra.2.3.5
/usr/bin/vdb-config
/usr/bin/vdb-config.2
/usr/bin/vdb-config.2.3.5
/usr/bin/vdb-copy
/usr/bin/vdb-copy.2
/usr/bin/vdb-copy.2.3.5
/usr/bin/vdb-decrypt
/usr/bin/vdb-decrypt.2
/usr/bin/vdb-decrypt.2.3.5
/usr/bin/vdb-dump
/usr/bin/vdb-dump.2
/usr/bin/vdb-dump.2.3.5
/usr/bin/vdb-encrypt
/usr/bin/vdb-encrypt.2
/usr/bin/vdb-encrypt.2.3.5
/usr/bin/vdb-lock
/usr/bin/vdb-lock.2
/usr/bin/vdb-lock.2.3.5
/usr/bin/vdb-passwd
/usr/bin/vdb-passwd.2
/usr/bin/vdb-passwd.2.3.5
/usr/bin/vdb-unlock
/usr/bin/vdb-unlock.2
/usr/bin/vdb-unlock.2.3.5
/usr/bin/vdb-validate
/usr/bin/vdb-validate.2
/usr/bin/vdb-validate.2.3.5
/usr/lib/ncbi/schema/454.vschema
/usr/lib/ncbi/schema/abi.vschema
/usr/lib/ncbi/schema/align.vschema
/usr/lib/ncbi/schema/built-in.vschema
/usr/lib/ncbi/schema/clip.vschema
/usr/lib/ncbi/schema/helicos.vschema
/usr/lib/ncbi/schema/illumina.vschema
/usr/lib/ncbi/schema/insdc.vschema
/usr/lib/ncbi/schema/ion-torrent.vschema
/usr/lib/ncbi/schema/ncbi.vschema
/usr/lib/ncbi/schema/pevents.vschema
/usr/lib/ncbi/schema/qstat.vschema
/usr/lib/ncbi/schema/refseq.vschema
/usr/lib/ncbi/schema/seq.vschema
/usr/lib/ncbi/schema/spotname.vschema
/usr/lib/ncbi/schema/sra.vschema
/usr/lib/ncbi/schema/stats.vschema
/usr/lib/ncbi/schema/vdb.vschema
/usr/lib/ncbi/schema/wgs-contig.vschema
/usr/share/doc/sra-toolkit/README
/usr/share/doc/sra-toolkit/changelog.Debian.gz
/usr/share/doc/sra-toolkit/copyright
/usr/share/doc/sra-toolkit/help/html/abi-dump-help.html
/usr/share/doc/sra-toolkit/help/html/abi-load-help.html
/usr/share/doc/sra-toolkit/help/html/bam-load-help.html
/usr/share/doc/sra-toolkit/help/html/copycat-help.html
/usr/share/doc/sra-toolkit/help/html/crc32sum-help.html
/usr/share/doc/sra-toolkit/help/html/fastq-dump-help.html
/usr/share/doc/sra-toolkit/help/html/fastq-load-help.html
/usr/share/doc/sra-toolkit/help/html/illumina-dump-help.html
/usr/share/doc/sra-toolkit/help/html/illumina-load-help.html
/usr/share/doc/sra-toolkit/help/html/kar-help.html
/usr/share/doc/sra-toolkit/help/html/kdbmeta-help.html
/usr/share/doc/sra-toolkit/help/html/kqsh-help.html
/usr/share/doc/sra-toolkit/help/html/md5cp-help.html
/usr/share/doc/sra-toolkit/help/html/rcexplain-help.html
/usr/share/doc/sra-toolkit/help/html/sff-dump-help.html
/usr/share/doc/sra-toolkit/help/html/sra-dump-help.html
/usr/share/doc/sra-toolkit/help/html/sra-stat-help.html
/usr/share/doc/sra-toolkit/help/html/srapath-help.html
/usr/share/doc/sra-toolkit/help/html/srf-load-help.html
/usr/share/doc/sra-toolkit/help/html/txt2kdb-help.html
/usr/share/doc/sra-toolkit/help/html/vdb-dump-help.html
/usr/share/doc/sra-toolkit/help/txt/abi-dump-help.txt
/usr/share/doc/sra-toolkit/help/txt/abi-load-help.txt
/usr/share/doc/sra-toolkit/help/txt/bam-loader-help.txt
/usr/share/doc/sra-toolkit/help/txt/copycat-help.txt
/usr/share/doc/sra-toolkit/help/txt/crc32sum-help.txt
/usr/share/doc/sra-toolkit/help/txt/fastq-dump-help.txt
/usr/share/doc/sra-toolkit/help/txt/fastq-load-help.txt
/usr/share/doc/sra-toolkit/help/txt/illumina-dump-help.txt
/usr/share/doc/sra-toolkit/help/txt/illumina-load-help.txt
/usr/share/doc/sra-toolkit/help/txt/kar-help.txt
/usr/share/doc/sra-toolkit/help/txt/kdbmeta-help.txt
/usr/share/doc/sra-toolkit/help/txt/kqsh-help.txt
/usr/share/doc/sra-toolkit/help/txt/md5cp-help.txt
/usr/share/doc/sra-toolkit/help/txt/rcexplain-help.txt
/usr/share/doc/sra-toolkit/help/txt/sff-dump-help.txt
/usr/share/doc/sra-toolkit/help/txt/sra-dump-help.txt
/usr/share/doc/sra-toolkit/help/txt/sra-stat-help.txt
/usr/share/doc/sra-toolkit/help/txt/srapath-help.txt
/usr/share/doc/sra-toolkit/help/txt/srf-load-help.txt
/usr/share/doc/sra-toolkit/help/txt/txt2kdb-help.txt
/usr/share/doc/sra-toolkit/help/txt/vdb-dump-help.txt

Changelog

2014-11-04 - Logan Rosen <logan@ubuntu.com>
sra-sdk (2.3.5-2+dfsg-1ubuntu1) vivid; urgency=medium
* Merge from Debian unstable. Remaining changes:
- debian/control: Limit to amd64 and i386 due to some assembly.
2014-07-30 - Andreas Tille <tille@debian.org>
sra-sdk (2.3.5-2+dfsg-1) unstable; urgency=medium
* New upstream version
* d/rules: Adapt get-orig-source target to new uscan implementation
* d/watch: use uversionmangle to get properly named download tarball
2014-04-26 - Logan Rosen <logan@ubuntu.com>
sra-sdk (2.3.4-2+dfsg-2ubuntu1) utopic; urgency=medium
* Merge from Debian unstable. Remaining changes:
- debian/control: Limit to amd64 and i386 due to some assembly.
2014-01-23 - Andreas Tille <tille@debian.org>
sra-sdk (2.3.4-2+dfsg-2) unstable; urgency=medium
* delete symbols file
Closes: #736411
* lintian override for no-symbols-control-file
2013-12-23 - Andreas Tille <tille@debian.org>
sra-sdk (2.3.4-2+dfsg-1) unstable; urgency=medium
* New upstream version
* debian/control:
- Add missing Depends: sra-toolkit-libs0 to sra-toolkit-libs-dev
Closes: #715133
- Standards-Version: 3.9.5 (no changes needed)
* debian/sra-toolkit-libs0.symbols: Adapted to new upstream version
2013-12-10 - Logan Rosen <logan@ubuntu.com>
sra-sdk (2.3.3-4~dfsg-1ubuntu1) trusty; urgency=low
* Merge from Debian unstable. Remaining changes:
- debian/control: Limit to amd64 and i386 due to some assembly.
2013-10-23 - Andreas Tille <tille@debian.org>
sra-sdk (2.3.3-4~dfsg-1) unstable; urgency=low
[ Andreas Tille ]
* New upstream version
* debian/upstream: Add citation information
* fix debian/watch
* debian/control:
- cme fix dpkg-control
- debhelper 9
- canonical Vcs fields
* debian/copyright: Exclude external libraries
* debian/rules:
- Add get-orig-source target to call enhances uscan
- remove override because upstream seems to do the correct thing now
- libsra-schema seems to be not built any more in this version so
drop the special handling of it
- Reactivate deletion of libs/krypto/*.pic.o.list files to get a
really clean source
* debian/doc: USAGE is not provided by upstream any more
* debian/patches/build-with-system-libbz2-libz.patch: Fix build problem
(thanks to Gert Wollny <gw.fossdev@gmail.com> for the patch)
* debian/sra-toolkit.install: There are neither mod?? nor wmod?? files
shipped in this version any more - so remove these from dh_install
* debian/patches/hardening.patch: Propagate Debian hardening options
into build system
* debian/patches/hardening-format-security.patch: Fix format strings in
snprintf() calls
* debian/watch: mangle version string
* debian/sra-toolkit-libs0.lintian-overrides: override
package-name-doesnt-match-sonames
[ Charles Plessy ]
32dd5cd Updated symbols file.
2012-06-14 - Ben Collins <bcollins@ubuntu.com>
sra-sdk (2.1.7a-1ubuntu2) quantal; urgency=low
* Fowl ball! Missed one package to be marked as amd64/i386 only.
2012-06-14 - Ben Collins <bcollins@ubuntu.com>
sra-sdk (2.1.7a-1ubuntu1) quantal; urgency=low
* Limit to amd64 and i386 due to some assembly.
2012-01-10 - Charles Plessy <plessy@debian.org>
sra-sdk (2.1.7a-1) unstable; urgency=low
[ Charles Plessy ]
61e22aa New upstream release (Closes: #627861).
1b09fd5 Normalised debian/copyright file with config-edit.
a93e7b5 Wildcard characters to match 64 or 32 according to the architecture.
3d66d80 New upstream source location in debian/watch.
74e5234 Mark the use of git-buildpackage by debian/gbp.conf.
0074d68 Simplified Homepage URL in debian/control.
5cd8039 Use a target that allows dynamic linking (debian/rules).
9815817 Do not install empty /usr/bin/ncbi directory (debian/rules).
fb42792 Updated debian/sra-toolkit-libs0.symbols.
866f773 Install config.kfg and vdb-copy.kfg in /etc/ncbi.
[ Andreas Tille ]
9e6e831 Suggest patches for build system to build on non i386&amd64
architectures as well as BSD and Hurd

See Also

Package Description
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sredird_2.2.1-1.1_amd64.deb RFC 2217 compliant Telnet serial port redirector
srf-doc_0.1+dfsg-4_all.deb specification documents for the SRF format DNA sequence data
srg_1.3.6-2ubuntu1_amd64.deb Fast, Flexible and Detailed log analysis for the Squid Proxy
srm-ifce-dev_1.23.3-1build1_amd64.deb SRM client side headers and development files
srptools_1.0.2-1_amd64.deb Tools for Infiniband attached storage (SRP)
srs_0.31-5_all.deb command-line Sender Rewriting Scheme client
srtp-docs_1.4.5~20130609~dfsg-1.1ubuntu1_all.deb Secure RTP (SRTP) and UST Reference Implementations - documentation
srtp-utils_1.4.5~20130609~dfsg-1.1ubuntu1_amd64.deb Secure RTP (SRTP) and UST Reference Implementations - utilities
ssake-examples_3.8.4-1_all.deb example data for SSAKE, a genomic assembler of short reads
ssake_3.8.4-1_all.deb genomics application for assembling millions of very short DNA sequences
ssdeep_2.13-2_amd64.deb recursive piecewise hashing tool
ssed_3.62-7_amd64.deb The super sed stream editor
ssft_0.9.13_all.deb Shell Scripts Frontend Tool
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