stacks_1.35-1ubuntu1_i386.deb


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Description

stacks - pipeline for building loci from short-read DNA sequences

Property Value
Distribution Ubuntu 16.04 LTS (Xenial Xerus)
Repository Ubuntu Universe i386
Package name stacks
Package version 1.35
Package release 1ubuntu1
Package architecture i386
Package type deb
Installed size 3.76 KB
Download size 741.46 KB
Official Mirror archive.ubuntu.com
Stacks is a software pipeline for building loci from short-read sequences,
such as those generated on the Illumina platform. Stacks was developed to work
with restriction enzyme-based data, such as RAD-seq, for the purpose of
building genetic maps and conducting population genomics and phylogeography.
Note that this package installs Stacks such that all commands must be run as:
$ stacks <cmdname> <args>

Alternatives

Package Version Architecture Repository
stacks_1.35-1ubuntu1_amd64.deb 1.35 amd64 Ubuntu Universe
stacks - - -

Requires

Name Value
libc6 >= 2.15
libdbi-perl -
libgcc1 >= 1:3.0
libgomp1 >= 4.9
libstdc++6 >= 5.2
samtools -
zlib1g >= 1:1.2.6

Download

Type URL
Binary Package stacks_1.35-1ubuntu1_i386.deb
Source Package stacks

Install Howto

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

Files

Path
/usr/bin/stacks
/usr/lib/debian-med/bin/clone_filter
/usr/lib/debian-med/bin/cstacks
/usr/lib/debian-med/bin/denovo_map
/usr/lib/debian-med/bin/denovo_map.pl
/usr/lib/debian-med/bin/estacks
/usr/lib/debian-med/bin/exec_velvet
/usr/lib/debian-med/bin/exec_velvet.pl
/usr/lib/debian-med/bin/export_sql
/usr/lib/debian-med/bin/export_sql.pl
/usr/lib/debian-med/bin/genotypes
/usr/lib/debian-med/bin/hstacks
/usr/lib/debian-med/bin/index_radtags
/usr/lib/debian-med/bin/index_radtags.pl
/usr/lib/debian-med/bin/kmer_filter
/usr/lib/debian-med/bin/load_radtags
/usr/lib/debian-med/bin/load_radtags.pl
/usr/lib/debian-med/bin/load_sequences
/usr/lib/debian-med/bin/load_sequences.pl
/usr/lib/debian-med/bin/phasedstacks
/usr/lib/debian-med/bin/populations
/usr/lib/debian-med/bin/process_radtags
/usr/lib/debian-med/bin/process_shortreads
/usr/lib/debian-med/bin/pstacks
/usr/lib/debian-med/bin/ref_map
/usr/lib/debian-med/bin/ref_map.pl
/usr/lib/debian-med/bin/rxstacks
/usr/lib/debian-med/bin/sort_read_pairs
/usr/lib/debian-med/bin/sort_read_pairs.pl
/usr/lib/debian-med/bin/sstacks
/usr/lib/debian-med/bin/stacks_export_notify
/usr/lib/debian-med/bin/stacks_export_notify.pl
/usr/lib/debian-med/bin/ustacks
/usr/lib/stacks/bin/clone_filter
/usr/lib/stacks/bin/cstacks
/usr/lib/stacks/bin/denovo_map
/usr/lib/stacks/bin/denovo_map.pl
/usr/lib/stacks/bin/estacks
/usr/lib/stacks/bin/exec_velvet
/usr/lib/stacks/bin/exec_velvet.pl
/usr/lib/stacks/bin/export_sql
/usr/lib/stacks/bin/export_sql.pl
/usr/lib/stacks/bin/genotypes
/usr/lib/stacks/bin/hstacks
/usr/lib/stacks/bin/index_radtags
/usr/lib/stacks/bin/index_radtags.pl
/usr/lib/stacks/bin/kmer_filter
/usr/lib/stacks/bin/load_radtags
/usr/lib/stacks/bin/load_radtags.pl
/usr/lib/stacks/bin/load_sequences
/usr/lib/stacks/bin/load_sequences.pl
/usr/lib/stacks/bin/phasedstacks
/usr/lib/stacks/bin/populations
/usr/lib/stacks/bin/process_radtags
/usr/lib/stacks/bin/process_shortreads
/usr/lib/stacks/bin/pstacks
/usr/lib/stacks/bin/ref_map
/usr/lib/stacks/bin/ref_map.pl
/usr/lib/stacks/bin/rxstacks
/usr/lib/stacks/bin/sort_read_pairs
/usr/lib/stacks/bin/sort_read_pairs.pl
/usr/lib/stacks/bin/sstacks
/usr/lib/stacks/bin/stacks_export_notify
/usr/lib/stacks/bin/stacks_export_notify.pl
/usr/lib/stacks/bin/ustacks
/usr/share/doc/stacks/README.Debian
/usr/share/doc/stacks/changelog.Debian.gz
/usr/share/doc/stacks/copyright

Changelog

2016-04-04 - Nishanth Aravamudan <nish.aravamudan@canonical.com>
stacks (1.35-1ubuntu1) xenial; urgency=medium
* Update to PHP7.0 dependencies (LP: #1565888).
2015-09-22 - Andreas Tille <tille@debian.org>
stacks (1.35-1) unstable; urgency=medium
* New upstream version
2015-07-27 - Andreas Tille <tille@debian.org>
stacks (1.34-1) unstable; urgency=medium
* New upstream version
2015-07-13 - Andreas Tille <tille@debian.org>
stacks (1.32-1) unstable; urgency=medium
* New upstream version
2015-02-19 - Andreas Tille <tille@debian.org>
stacks (1.25-1) unstable; urgency=medium
* Initial upload to Debian
Closes: #778832
2015-02-19 - Tim Booth <tbooth@ceh.ac.uk>
stacks (1.25-0biolinux2) trusty; urgency=medium
* Correct silly cut-and-paste-o in control file
2015-02-18 - Tim Booth <tbooth@ceh.ac.uk>
stacks (1.25-0biolinux1) trusty; urgency=medium
* New upstream
* Re-work stacks-setup-database to make databases named by project
* ...and to enable database deletion
* Improve the help you get from "stacks help"
2015-01-29 - Tim Booth <tbooth@ceh.ac.uk>
stacks (1.24-0ubuntu4) trusty; urgency=medium
* Change web path back to /stacks rather than stacks-web,
just leaving the Apache config fragment with that name.
2015-01-23 - Tim Booth <tbooth@ceh.ac.uk>
stacks (1.24-0ubuntu3) trusty; urgency=low
* Set PATH before calling any Stacks program in the wrapper
2015-01-15 - Tim Booth <tbooth@ceh.ac.uk>
stacks (1.24-0ubuntu2) trusty; urgency=medium
* Initial release.
* Make stacks package plus stack-web for the web stuff
* Require sparsehash >2

See Also

Package Description
staden-common_2.0.0+b10-4ubuntu1_all.deb Architecture independent files for Staden
staden-io-lib-examples_1.14.6-2_all.deb programs for maniuplating DNA sequencing files (usage examples)
staden-io-lib-utils_1.14.6-2_i386.deb programs for maniuplating DNA sequencing files
staden_2.0.0+b10-4ubuntu1_i386.deb DNA sequence assembly (Gap4/Gap5), editing and analysis tools
stalin_0.11-6_i386.deb An extremely aggressive Scheme compiler
stalonetray_0.8.1-1_i386.deb Standalone freedesktop.org and KDE systray implementation
stardata-common_0.8_i386.deb Common framework to manage astronomy packages
stardict-common_3.0.1-9.2ubuntu3_all.deb International dictionary - data files
stardict-czech_20140101-3_all.deb Stardict package for Czech dictionary of foreign words
stardict-gnome_3.0.1-9.2ubuntu3_i386.deb International dictionary for GNOME 2
stardict-gtk_3.0.1-9.2ubuntu3_i386.deb International dictionary written in GTK+ 2.x
stardict-plugin-espeak_3.0.1-9.2ubuntu3_i386.deb International dictionary - eSpeak TTS plugin
stardict-plugin-festival_3.0.1-9.2ubuntu3_i386.deb International dictionary - Festival TTS plugin
stardict-plugin-spell_3.0.1-9.2ubuntu3_i386.deb International dictionary - spell plugin
stardict-plugin_3.0.1-9.2ubuntu3_i386.deb International dictionary - common plugins
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