tophat_2.1.1+dfsg1-2+b1_amd64.deb


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Description

tophat - fast splice junction mapper for RNA-Seq reads

Property Value
Distribution Debian Sid
Repository Debian Main amd64
Package name tophat
Package version 2.1.1+dfsg1
Package release 2+b1
Package architecture amd64
Package type deb
Installed size 3.74 KB
Download size 654.17 KB
Official Mirror ftp.br.debian.org
Description -

Alternatives

Package Version Architecture Repository
tophat - - -

Requires

Name Value
bowtie -
bowtie2 -
libboost system1.67.0
libboost thread1.67.0
libc6 >= 2.15
libgcc1 >= 1:3.0
libstdc++6 >= 5.2
python -
samtools >= 1.5
zlib1g >= 1:1.2.3.3

Download

Type URL
Binary Package tophat_2.1.1+dfsg1-2+b1_amd64.deb
Source Package tophat

Install Howto

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

Files

Path
/usr/bin/bam2fastx
/usr/bin/bam_merge
/usr/bin/bed_to_juncs
/usr/bin/contig_to_chr_coords
/usr/bin/fix_map_ordering
/usr/bin/gtf_juncs
/usr/bin/gtf_to_fasta
/usr/bin/juncs_db
/usr/bin/long_spanning_reads
/usr/bin/map2gtf
/usr/bin/prep_reads
/usr/bin/sam_juncs
/usr/bin/segment_juncs
/usr/bin/sra_to_solid
/usr/bin/tophat
/usr/bin/tophat-fusion-post
/usr/bin/tophat2
/usr/bin/tophat_reports
/usr/share/doc/tophat/README
/usr/share/doc/tophat/README.test
/usr/share/doc/tophat/changelog.Debian.amd64.gz
/usr/share/doc/tophat/changelog.Debian.gz
/usr/share/doc/tophat/copyright
/usr/share/doc/tophat/run-unit-test
/usr/share/doc/tophat/test_data/reads_1.fq.gz
/usr/share/doc/tophat/test_data/reads_2.fq.gz
/usr/share/doc/tophat/test_data/test_ref.1.bt2.gz
/usr/share/doc/tophat/test_data/test_ref.1.ebwt.gz
/usr/share/doc/tophat/test_data/test_ref.2.bt2
/usr/share/doc/tophat/test_data/test_ref.2.ebwt
/usr/share/doc/tophat/test_data/test_ref.3.bt2
/usr/share/doc/tophat/test_data/test_ref.4.bt2
/usr/share/doc/tophat/test_data/test_ref.fa
/usr/share/doc/tophat/test_data/test_ref.rev.1.bt2.gz
/usr/share/doc/tophat/test_data/test_ref.rev.1.ebwt.gz
/usr/share/doc/tophat/test_data/test_ref.rev.2.bt2
/usr/share/doc/tophat/test_data/test_ref.rev.2.ebwt
/usr/share/man/man1/bam2fastx.1.gz
/usr/share/man/man1/bed_to_juncs.1.gz
/usr/share/man/man1/contig_to_chr_coords.1.gz
/usr/share/man/man1/tophat.1.gz

Changelog

2018-08-18 - Andreas Tille <tille@debian.org>
tophat (2.1.1+dfsg1-2) unstable; urgency=medium
* Fix Makefile.am
Closes: #906510
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.0
* Remove unneeded get-orig-source target
2017-12-06 - Fabian Klötzl <fabian@kloetzl.info>
tophat (2.1.1+dfsg1-1) unstable; urgency=medium
* Team upload
* debian/upstream/metadata:
- Added references to registries
- yamllint cleanliness
[ Nadiya Sitdykova ]
* add info about debian/tests/test_data
[ Fabian Klötzl ]
* remove convenience copy of samtools.
Closes: #780816
* adapt tophat script to recent samtools version
[ Andreas Tille ]
* Remove unused license paragraph
* Standards-Version: 4.1.1
* Really remove samtools code copy also from source tarball
* Versioned Depends: samtools (>= 1.5)
* d/watch: enable numbered dfsg-appendices
2017-09-04 - Andreas Tille <tille@debian.org>
tophat (2.1.1+dfsg-4) unstable; urgency=medium
* Build-Depends: bowtie + Architecture: any
Closes: #873866
* Standards-Version: 4.1.0 (no changes needed)
* Autoreconf is default with debhelper 10
2017-07-14 - Nadiya Sitdykova <rovenskasa@gmail.com>
tophat (2.1.1+dfsg-3) unstable; urgency=medium
* Team upload.
[ Nadiya Sitdykova ]
* Add autopkgtest test-suite 
[ Andreas Tille ]
* debhelper 10 (use --no-parallel to avoid build problems)
* Standards-Version: 4.0.0 (no changes needed)
* Drop unneeded gbp.conf
* d/rules: use DEB_SOURCE
2016-05-14 - Sascha Steinbiss <sascha@steinbiss.name>
tophat (2.1.1+dfsg-2) unstable; urgency=medium
[ Sascha Steinbiss ]
* Team upload.
* Fix building with GCC 6.
Closes: #811881.
[ Andreas Tille ]
* cme fix dpkg-control
2016-03-17 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
tophat (2.1.1+dfsg-1) unstable; urgency=medium
* Imported Upstream version 2.1.1+dfsg
* Refresh and delete unused patches
* Apply cme fix dpkg
* Export additional hardening flags - hardening=+all
* Don't install 3rd party software (intervaltree,sortedcontainers)
* Fix Makefile for the embedded copy of samtools-0.1.18
* d/copyright:
- Add Files: stanza for samtools-0.1.18
- Add to Files-Excluded: intervaltree and sortedcontainers
- Fix Source url
2015-07-18 - Andreas Tille <tille@debian.org>
tophat (2.1.0+dfsg-1) unstable; urgency=medium
* New upstream version
2015-04-29 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
tophat (2.0.14+dfsg-1) unstable; urgency=medium
* Imported Upstream version 2.0.14+dfsg
* d/patches: applied cme fix dpkg, s/Descriptions/Description/
2014-10-26 - Alexandre Mestiashvili <alex@biotec.tu-dresden.de>
tophat (2.0.13+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* Adapted patches
[ Alexandre Mestiashvili]
* debian/patches/hardening4samtols.patch: add hardening flags for 
embedded copy of samtools
2014-09-25 - Andreas Tille <tille@debian.org>
tophat (2.0.12+dfsg-3) unstable; urgency=medium
* Since tophat depends from bowtie|bowtie2 and now both versions
are available only on amd64 tophat itself is also
Architecture: amd64 kfreebsd-amd64
* Do not "Suggests: bowtie" since it is just in "Depends"
* cme fix dpkg-control
* d/copyright: fix "empty-short-license-in-dep5-copyright" lintian
warnings

See Also

Package Description
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topp_2.4.0-real-1_amd64.deb set of programs implementing The OpenMS Proteomic Pipeline
toppler_1.1.6-3_amd64.deb clone of the "Nebulus" game on old 8 and 16 bit machines
toppred_1.10-7_amd64.deb transmembrane topology prediction
tor-arm_2.1.0-2_all.deb transitional package
tor-geoipdb_0.3.5.8-1_all.deb GeoIP database for Tor
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tora_2.1.3-4_amd64.deb graphical toolkit for database developers and administrators
torch-core-free_20171127_amd64.deb Scientific Computing Framework For Luajit (Core Components)
torch-trepl_0~20170619-ge5e17e3-7_all.deb REPL Wrapper Package for Torch Framework
torcs-data_1.3.7+dfsg-4_all.deb data files for TORCS
torcs_1.3.7+dfsg-4_amd64.deb 3D racing cars simulator game using OpenGL
torrus-common_3.00-1_all.deb Universal front-end for Round-Robin Databases (common files)
torsocks_2.3.0-1_amd64.deb use SOCKS-friendly applications with Tor
tortoisehg-caja_4.8.1-0.1_all.deb Graphical tool for working with Mercurial (Caja extension)
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