pbgenomicconsensus_2.3.2-5_all.deb


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Description

pbgenomicconsensus - Pacific Biosciences variant and consensus caller

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename pbgenomicconsensus_2.3.2-5_all.deb
Package name pbgenomicconsensus
Package version 2.3.2
Package release 5
Package architecture all
Package type deb
Category universe/science
Homepage https://github.com/PacificBiosciences/GenomicConsensus
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 30.47 KB
Installed size 76.00 KB
The GenomicConsensus package provides Quiver, Pacific Biosciences'
flagship consensus and variant caller. Quiver is an algorithm that finds
the maximum likelihood template sequence given PacBio reads of the template.
These reads are modeled using a conditional random field approach that
prescribes a probability to a read given a template sequence. In addition to
the base sequence of each read, Quiver uses several additional quality value
covariates that the base caller provides.
This package is part of the SMRTAnalysis suite

Alternatives

Package Version Architecture Repository
pbgenomicconsensus_2.3.2-5_all.deb 2.3.2 all Ubuntu Universe
pbgenomicconsensus - - -

Requires

Name Value
python-pbgenomicconsensus = 2.3.2-5
python-pkg-resources -
python:any -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package pbgenomicconsensus_2.3.2-5_all.deb
Source Package pbgenomicconsensus

Install Howto

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

Files

Path
/usr/bin/arrow
/usr/bin/gffToBed
/usr/bin/gffToVcf
/usr/bin/plurality
/usr/bin/quiver
/usr/bin/summarizeConsensus
/usr/bin/variantCaller
/usr/share/doc/pbgenomicconsensus/FAQ.rst.gz
/usr/share/doc/pbgenomicconsensus/NEWS.Debian.gz
/usr/share/doc/pbgenomicconsensus/README.md
/usr/share/doc/pbgenomicconsensus/changelog.Debian.gz
/usr/share/doc/pbgenomicconsensus/copyright
/usr/share/doc/pbgenomicconsensus/examples/params-template.xml
/usr/share/man/man1/arrow.1.gz
/usr/share/man/man1/gffToBed.1.gz
/usr/share/man/man1/gffToVcf.1.gz
/usr/share/man/man1/plurality.1.gz
/usr/share/man/man1/quiver.1.gz
/usr/share/man/man1/summarizeConsensus.1.gz
/usr/share/man/man1/variantCaller.1.gz
/usr/share/man/man5/pbgff.5.gz
/usr/share/man/man7/genomicconsensus.7.gz

Changelog

2019-04-07 - Liubov Chuprikova <chuprikovalv@gmail.com>
pbgenomicconsensus (2.3.2-5) unstable; urgency=medium
* Team upload.
* Fix autopkgtest dependencies
Closes: #925909
2019-04-06 - Andreas Tille <tille@debian.org>
pbgenomicconsensus (2.3.2-4) unstable; urgency=medium
* Fix dependencies
Closes: #925909
* unset GZIP in autopkgtest
2019-04-02 - Andreas Tille <tille@debian.org>
pbgenomicconsensus (2.3.2-3) unstable; urgency=medium
* Really fix autopkgtest
2019-04-02 - Andreas Tille <tille@debian.org>
pbgenomicconsensus (2.3.2-2) unstable; urgency=medium
[ Afif Elghraoui ]
* Remove myself from Uploaders
[ Andreas Tille ]
* Add myself to Uploaders
* python-pbgenomicconsensus Depends: python-pbconsensuscore
* Test Depends: poa
* Ignore some warnings which are breaking test results, remove
tests that are based on non-existing input data
* Move exclusion of tests to upstream Makefile via patch rather than
in d/rules.  This is needed to run autopkgtest successfully
Closes: #925909
2019-01-11 - Andreas Tille <tille@debian.org>
pbgenomicconsensus (2.3.2-1) unstable; urgency=medium
* Team upload
[ Afif Elghraoui ]
* New upstream release snapshot
(git 0d51d50, 2018-03-07)
* Add README.source explaining how to select upstream snapshots
[ Andreas Tille ]
* debhelper 12
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.3.0
* Build-Depends: python-pytest
* Build-Depends: python-consensuscore2 (to be uploaded, see ITP #847310)
* Respect DEB_BUILD_OPTIONS in override_dh_auto_test
* Several changes to make test suite work
* Pre-create manpages (seems there is no point in calling pandoc inside
build process.)
* Remove unused lintian-override
2017-01-21 - Afif Elghraoui <afif@debian.org>
pbgenomicconsensus (2.1.0-1) unstable; urgency=medium
* New upstream release snapshot
(git 5893b16, 2016-07-19)
* Update manpage for new release
* Adapt test suite for missing pbtestdata
* autopkgtest: make sure to test installed version of the package
* Add python-consensuscore2 to Recommends
* Add lintian override for autopkgtest dependency list
* Install FAQ into docs rather than as a manpage
2016-07-16 - Afif Elghraoui <afif@debian.org>
pbgenomicconsensus (2.0.0+20160420-2) unstable; urgency=low
* Remove convenience script for poa (Closes: #831220)
2016-07-08 - Afif Elghraoui <afif@debian.org>
pbgenomicconsensus (2.0.0+20160420-1) unstable; urgency=medium
* Imported Upstream version 2.0.0+20160420 (upstream git 782a362)
(Closes: #830358)
* Add explicit, versioned build-dependencies
* Install python scripts at build time rather than patching setup.py
* Redo and reorganize manpages
* Bump Standards-Version to 3.9.8
* Suggest consensuscore2
* Install new examples
2016-02-12 - Afif Elghraoui <afif@ghraoui.name>
pbgenomicconsensus (2.0.0+20151210-1) unstable; urgency=medium
* Imported Upstream version 2.0.0+20151210
(corresponds to upstream release tag "smrtanalysis-3.0.2")
* Update patches
* Revise debian/*.install file to not be so specific
* Remove manpage for nonexistent script
* Add dependency on pbcommand
* Add strict dependency on same version of backend library from same package
* Rename manpages to match executables where language extensions dropped upstream
* Add NEWS file to advise users of renamed scripts
* Use secure VCS URLs in debian/control
2015-11-24 - Afif Elghraoui <afif@ghraoui.name>
pbgenomicconsensus (1.1.0-1) unstable; urgency=medium
* Imported Upstream version 1.1.0 (untagged release: bee9a1f from Jun 24)

See Also

Package Description
pbh5tools_0.8.0+git20170929.58d54ff+dfsg-1_all.deb tools for manipulating Pacific Biosciences HDF5 files
pbsim_1.0.3+git20180330.e014b1d+dfsg-1_amd64.deb simulator for PacBio sequencing reads
pbuilder-scripts_22_all.deb Wrapper scripts for pbuilder
pbuilder_0.230.4_all.deb personal package builder for Debian packages
pbzip2_1.1.9-1build1_amd64.deb parallel bzip2 implementation
pcal_4.11.0-3build1_amd64.deb generate Postscript calendars without X
pcalendar_3.4.1-3_all.deb track menstrual cycles and predict fertility periods
pcapfix_1.1.4-2_amd64.deb repairs broken pcap and pcapng files
pcaputils_0.8-1build1_amd64.deb specialized libpcap utilities
pcb-common_4.2.0-2_all.deb printed circuit board (pcb) design program - common files
pcb-gtk_4.2.0-2_amd64.deb printed circuit board (pcb) design program - GTK+ interface
pcb-lesstif_4.2.0-2_amd64.deb printed circuit board (pcb) design program - LessTif interface
pcb-rnd_2.1.1-1_amd64.deb Modular Printed Circuit Board layout tool
pcb2gcode_1.1.4-git20120902-1.1build3_amd64.deb command-line tool for engraving PCBs using CNCs
pcb_4.2.0-2_all.deb printed circuit board (pcb) design program - metapackage
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