stacks_1.35-1ubuntu1_i386.deb


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Description

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

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

    Download

    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

    • /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

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