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Open-Source — ultimaker (Ultimaker) / debian-backup — Project

A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.

Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

parsnp 1.2+dfsg-5

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One-liner (summary)

rapid core genome multi-alignment

Description

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.

License

Unknown

Size

508.8 KB

Downloads

Status	Completed
Checksum (MD5)	9736bd2159da6914cfa757f17b70c768
Checksum (SHA-1)	92dc16d9d087ccd8e7c2cb729e4e43c6d7a9fd92
Checksum (SHA-256)	8b0f04cb4acdb54fdd6ae3ed3307c473a7670f469fd4d8a9135eaf2ff66d1a48
Checksum (SHA-512)	d861067f3d6bee17615153713f0b6bc550e27001d3a30835363ff16f7eb32f9f74…
GPG Signature	Download
GPG Fingerprint	c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution	debian/buster - Debian - 10 (Buster)
Storage Region	Dublin, Ireland
Type	Binary (contains binaries and binary artifacts)
Uploaded At	4 months ago
Uploaded By
Slug Id	parsnp_12dfsg-5_arm64deb-4xq1
Unique Id	FoOHZEPTQQAx
Version (Raw)	1.2+dfsg-5
Version (Parsed)	Major: 1 Minor: 2 Type: SemVer (Compat) Metadata: dfsg-5
	extended metadata
Homepage	http://harvest.readthedocs.org/en/latest/content/parsnp.html
Installed Size	873.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

ca2a190a28c724251c90660429d88522

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

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[![This version of 'parsnp' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'parsnp' @ Cloudsmith|
.. |This version of 'parsnp' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'parsnp' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/1.2+dfsg-5/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'parsnp' @ Cloudsmith" /></a>

rendered as:

To embed the badge for the latest package version, use the following:

[![Latest version of 'parsnp' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 'parsnp' @ Cloudsmith|
.. |Latest version of 'parsnp' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'parsnp' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/parsnp/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 'parsnp' @ Cloudsmith" /></a>

rendered as:

These instructions assume you have setup the repository first (or read it).

To install/use parsnp @ version 1.2+dfsg-5 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update

sudo apt-get install parsnp=1.2+dfsg-5

Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.

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