abyss_1.9.0-1build1_amd64.deb


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Description

abyss - de novo, parallel, sequence assembler for short reads

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Multiverse amd64
Package name abyss
Package version 1.9.0
Package release 1build1
Package architecture amd64
Package type deb
Installed size 6.58 KB
Download size 1.21 MB
Official Mirror archive.ubuntu.com
ABySS is a de novo, parallel, sequence assembler that is designed for
short reads. It may be used to assemble genome or transcriptome
sequence data. Parallelization is achieved using MPI, OpenMP and
pthread.

Alternatives

Package Version Architecture Repository
abyss_1.9.0-1build1_i386.deb 1.9.0 i386 Ubuntu Multiverse
abyss - - -

Requires

Name Value
libc6 >= 2.14
libgcc1 >= 1:4.0
libgomp1 >= 4.9
libopenmpi1.10 -
libsqlite3-0 >= 3.5.9
libstdc++6 >= 5.2
make -
perl -

Download

Type URL
Binary Package abyss_1.9.0-1build1_amd64.deb
Source Package abyss

Install Howto

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

Files

Path
/usr/bin/DistanceEst
/usr/bin/abyss-fixmate
/usr/bin/abyss-pe
/usr/lib/abyss/ABYSS
/usr/lib/abyss/ABYSS-P
/usr/lib/abyss/AdjList
/usr/lib/abyss/Consensus
/usr/lib/abyss/DAssembler
/usr/lib/abyss/DistanceEst
/usr/lib/abyss/DistanceEst-ssq
/usr/lib/abyss/KAligner
/usr/lib/abyss/MergeContigs
/usr/lib/abyss/MergePaths
/usr/lib/abyss/Overlap
/usr/lib/abyss/ParseAligns
/usr/lib/abyss/PathConsensus
/usr/lib/abyss/PathOverlap
/usr/lib/abyss/PopBubbles
/usr/lib/abyss/SimpleGraph
/usr/lib/abyss/abyss-align
/usr/lib/abyss/abyss-bloom
/usr/lib/abyss/abyss-bloom-dist.mk
/usr/lib/abyss/abyss-bowtie
/usr/lib/abyss/abyss-bowtie2
/usr/lib/abyss/abyss-bwa
/usr/lib/abyss/abyss-bwamem
/usr/lib/abyss/abyss-bwasw
/usr/lib/abyss/abyss-db-csv
/usr/lib/abyss/abyss-db-txt
/usr/lib/abyss/abyss-dida
/usr/lib/abyss/abyss-fac
/usr/lib/abyss/abyss-fatoagp
/usr/lib/abyss/abyss-filtergraph
/usr/lib/abyss/abyss-fixmate
/usr/lib/abyss/abyss-fixmate-ssq
/usr/lib/abyss/abyss-gapfill
/usr/lib/abyss/abyss-gc
/usr/lib/abyss/abyss-index
/usr/lib/abyss/abyss-junction
/usr/lib/abyss/abyss-kaligner
/usr/lib/abyss/abyss-layout
/usr/lib/abyss/abyss-longseqdist
/usr/lib/abyss/abyss-map
/usr/lib/abyss/abyss-map-ssq
/usr/lib/abyss/abyss-mergepairs
/usr/lib/abyss/abyss-overlap
/usr/lib/abyss/abyss-paired-dbg
/usr/lib/abyss/abyss-paired-dbg-mpi
/usr/lib/abyss/abyss-pe
/usr/lib/abyss/abyss-samtoafg
/usr/lib/abyss/abyss-scaffold
/usr/lib/abyss/abyss-sealer
/usr/lib/abyss/abyss-tabtomd
/usr/lib/abyss/abyss-todot
/usr/lib/abyss/abyss-tofastq
/usr/lib/abyss/konnector
/usr/lib/abyss/logcounter
/usr/share/doc/abyss/README.css
/usr/share/doc/abyss/README.html
/usr/share/doc/abyss/README.md.gz
/usr/share/doc/abyss/changelog.Debian.gz
/usr/share/doc/abyss/copyright
/usr/share/doc/abyss/flowchart.pdf.gz
/usr/share/man/man1/ABYSS.1.gz
/usr/share/man/man1/abyss-pe.1.gz
/usr/share/man/man1/abyss-tofastq.1.gz

Changelog

2016-02-07 - Matthias Klose <doko@ubuntu.com>
abyss (1.9.0-1build1) xenial; urgency=medium
* No-change rebuild for openmpi transition.
2015-07-16 - Andreas Tille <tille@debian.org>
abyss (1.9.0-1) unstable; urgency=medium
* New upstream version
Adapted patches
* Took over COPYRIGHT from upstream as debian/copyright
* Dropped Shaun Jackman from Uploaders since he confirmed that he will not
be able to maintain the package
* Build-Depends: libsqlite3-dev
* Script uses bash syntax so request bash interpreter
2015-05-18 - Andreas Tille <tille@debian.org>
abyss (1.5.2-2) unstable; urgency=medium
* abyss-fixmate and DistanceEst are expected to be in /usr/bin by sga
* configure was missing ghc -> mention this fact in README.source for
further inspection
* Fix FTBFS on 32-bit architectures (thanks for the patch to Graham
Inggs <graham@nerve.org.za>)
Closes: #780409
* cme fix dpkg-control
2014-09-15 - Andreas Tille <tille@debian.org>
abyss (1.5.2-1) unstable; urgency=medium
* New upstream version (remove applied patches)
* d/watch: Moved to github
* d/control+d/rules: use dh-autoreconf
* d/control: Build-Depends: libtext-multimarkdown-perl
* cme fix dpkg-control
* d/control: Build-Depends: libgtest-dev to enable unit tests at build time
* d/control: drop copy of citation info from long description
* patch to make gtest work (thanks to Anthony Raymond <traymond@bcgsc.ca>)
* Drop privacy breach in doc
2013-09-08 - Charles Plessy <plessy@debian.org>
abyss (1.3.6-1) unstable; urgency=low
* Team upload (Closes: #722072).
e05ee57 Imported Upstream version 1.3.5
b391f1f Imported Upstream version 1.3.6 (Closes: #702440)
7edc28b Signal the use of git-buildpackage with this configuration file.
a3beaac Normalised source package control file with config-model-edit.
dd86394 Conforms with Policy version 3.9.4.
71d42ad Normalised VCS URLs.
2013-07-01 - Dmitrijs Ledkovs <dmitrij.ledkov@ubuntu.com>
abyss (1.3.4-4) unstable; urgency=low
* Team upload.
* Fix FTBFS with gcc-4.8, -Werror=unused-local-typedefs.
* Enable parallel build.
2013-01-04 - Andreas Tille <tille@debian.org>
abyss (1.3.4-3) unstable; urgency=low
* Disable POPCNT
Closes: #697344
* Add debian/README.debian to inform users about this change asking
for some comparison of the speed to consider other means for better
performance
2012-06-01 - Andreas Tille <tille@debian.org>
abyss (1.3.4-2) unstable; urgency=low
* Team upload
* debian/upstream: BibTeX compliant authors
2012-05-31 - Shaun Jackman <sjackman@debian.org>
abyss (1.3.4-1) unstable; urgency=low
* New upstream release.
* debian/copyright: Add CityHash, which has an Expat license.
* debian/control: Bump Standards-Version to 3.9.3.1.
2012-04-01 - Andreas Tille <tille@debian.org>
abyss (1.3.3-2) unstable; urgency=low
* debian/control:
- Team maintenance in Debian Med team
- Moved packaging to Git
* debian/upstream: Add citation information
* debhelper 9 (control+compat)
* debian/copyright: Add github as another location for obtaining
the source

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