parsnp_1.2+dfsg-5_amd64.deb


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Description

parsnp - rapid core genome multi-alignment

Property Value
Distribution Ubuntu 19.04 (Disco Dingo)
Repository Ubuntu Universe amd64
Package filename parsnp_1.2+dfsg-5_amd64.deb
Package name parsnp
Package version 1.2+dfsg
Package release 5
Package architecture amd64
Package type deb
Category universe/science
Homepage http://harvest.readthedocs.org/en/latest/content/parsnp.html
License -
Maintainer Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
Download size 516.62 KB
Installed size 913.00 KB
Parsnp was designed to align the core genome of hundreds to thousands of
bacterial genomes within a few minutes to few hours. Input can be both
draft assemblies and finished genomes, and output includes variant (SNP)
calls, core genome phylogeny and multi-alignments. Parsnp leverages
contextual information provided by multi-alignments surrounding SNP
sites for filtration/cleaning, in addition to existing tools for
recombination detection/filtration and phylogenetic reconstruction.

Alternatives

Package Version Architecture Repository
parsnp_1.2+dfsg-5_i386.deb 1.2+dfsg i386 Ubuntu Universe
parsnp - - -

Requires

Name Value
fasttree -
libc6 >= 2.27
libgcc1 >= 1:3.0
libgomp1 >= 4.9
libmuscle1 >= 3.7+4565
libstdc++6 >= 5.2
mummer -
phipack -
python-numpy -
python:any -

Download

Type URL
Mirror archive.ubuntu.com
Binary Package parsnp_1.2+dfsg-5_amd64.deb
Source Package parsnp

Install Howto

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

Files

Path
/usr/bin/parsnp
/usr/lib/parsnp/parsnp
/usr/share/doc/parsnp/changelog.Debian.gz
/usr/share/doc/parsnp/copyright
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_12_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_15_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_16_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_17_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_18_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_19_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_1_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_21_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_25_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_2_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_3_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Al-Hasa_4_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Bisha_1_2012.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Buraidah_1_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/EMC_2012.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/England-Qatar_2012.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/England1.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/FRA-UAE.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Hafr-Al-Batin_1_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Hafr-Al-Batin_2_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Hafr-Al_Batin_6_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Indiana-USA-1_Saudi_Arabia_2014.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jeddah_1_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jeddah_2014_C7149.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jeddah_2014_C7569.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jeddah_2014_C7770.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Jordan-N3_2012.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KF192507.1.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KFU-HKU_1.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KFU-HKU_13.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KFU-HKU_19Dam.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KJ477102.1.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-363.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-376.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-378.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-503.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/KSA-CAMEL-505.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/NC_019843.2.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Qatar3.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Qatar4.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_14_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_1_2012.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_2_2012.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_3_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_4_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_5_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Riyadh_9_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Taif_1_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/genomes/Wadi-Ad-Dawasir_1_2013.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/ref/England1.fna.gz
/usr/share/doc/parsnp/examples/mers_virus/ref/England1.gbk.gz
/usr/share/man/man1/parsnp.1.gz
/usr/share/parsnp/Parsnp.py
/usr/share/parsnp/template.ini
/usr/share/python/runtime.d/parsnp.rtupdate

Changelog

2018-07-18 - Andreas Tille <tille@debian.org>
parsnp (1.2+dfsg-5) unstable; urgency=medium
* Build-Depends: dh-python
* libmuscle-3.7-dev is now libmuscle-dev
2018-07-17 - Andreas Tille <tille@debian.org>
parsnp (1.2+dfsg-4) unstable; urgency=medium
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* Remove ancient x-python-version field
* d/rules: do not parse d/changelog
2016-11-23 - Andreas Tille <tille@debian.org>
parsnp (1.2+dfsg-3) unstable; urgency=medium
* Fix build when trying to link with -Wl, --as-needed (Thanks for the patch
to Graham Inggs <ginggs@debian.org>)
Closes: #845415
* debhelper 10
* d/watch: version=4
2016-10-11 - Sascha Steinbiss <satta@debian.org>
parsnp (1.2+dfsg-2) unstable; urgency=medium
* Team upload.
[ Andreas Tille ]
* Add copyright statement at ftpmaster request
[ Sascha Steinbiss ]
* Drop -m64 from CXXFLAGS.
This addresses FTBFS on 32-bit systems. Thanks to Aaron M. Ucko for
the hint.
Closes: #838174
2016-07-21 - Andreas Tille <tille@debian.org>
parsnp (1.2+dfsg-1) unstable; urgency=medium
* Initial release (Closes: #831995)

See Also

Package Description
partclone_0.3.11-1build3_amd64.deb Utility to clone and restore a partition
partimage-doc_20050720-4_all.deb Partition Image User Documentation
partimage-server_0.6.9-7_amd64.deb server to use partimage across a network
partimage_0.6.9-7_amd64.deb backup partitions into a compressed image file
partitionmanager_3.3.1-5_amd64.deb file, disk and partition management for KDE
pasaffe_0.51-0ubuntu1_all.deb Password manager for GNOME
pasco_20040505-3_amd64.deb Internet Explorer cache forensic analysis tool
pasdoc_0.15.0-1_amd64.deb documentation tool for Pascal source code
pasmo_0.5.3-6build1_amd64.deb easy to use Z80 cross-assembler
pass-extension-otp_1.2.0-1_all.deb pass extension for managing one-time-password tokens
pass-extension-tail_1.1.1-2_all.deb password-store extension to avoid printing the password
pass-extension-tomb-basic_0.0.1+20170729+7512ad6-3_all.deb lightweight directory-based password manager (tomb extension)
pass-extension-tomb_1.1-4_all.deb lightweight directory-based password manager (tomb extension)
pass-git-helper_0.4-1_all.deb Git credential helper interfacing with pass
pass_1.7.3-2_all.deb lightweight directory-based password manager
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