sra-toolkit_2.3.5-2+dfsg-1ubuntu1_i386.deb


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Description

sra-toolkit - utilities for the NCBI Sequence Read Archive

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe i386
Package name: sra-toolkit
Package version: 2.3.5
Package release: 2+dfsg-1ubuntu1
Package architecture: i386
Package type: deb
Installed size: 5.18 KB
Download size: 969.73 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

    Download

    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

    • /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

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