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 10 (Buster)
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
TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra
high-throughput short read aligner Bowtie, and then analyzes the
mapping results to identify splice junctions between exons.
TopHat is a collaborative effort between the University of Maryland
Center for Bioinformatics and Computational Biology and the
University of California, Berkeley Departments of Mathematics and
Molecular and Cell Biology.

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

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