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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).

clonalframe 1.2-9

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One-liner (summary)

inference of bacterial microevolution using multilocus sequence data

Description

ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, it is recommend to use Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.

License

Unknown

Size

40.7 KB

Downloads

Status	Completed
Checksum (MD5)	4a17ee9220ce88bf105af597c5ae04bd
Checksum (SHA-1)	2cd91e7f90623e05c960461c671db6b1b0b301c9
Checksum (SHA-256)	1b90fdcfb0663b3850d8252176a591502ec6d11e8aa7b53262b0379550051b17
Checksum (SHA-512)	4eef15989d99275880835119b79519d4d422ffb25e21d9c855b34e8e08ecb491b6…
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	1 year, 1 month ago
Uploaded By
Slug Id	clonalframe_12-9_armhfdeb-gpv6
Unique Id	ZAhl76WHSwCI
Version (Raw)	1.2-9
Version (Parsed)	Major: 1 Minor: 2 Pre (Str): (empty) Pre (Num Array): 9 Type: SemVer (Compat)
	extended metadata
Homepage	http://www.xavierdidelot.xtreemhost.com/clonalframe.htm
Installed Size	82.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

46ade7176adb87fce00bc25e9b051c88

Depends	libc6	>=2.4
Depends	libgcc1	>=1:3.5
Depends	libgsl23	>=2.5
Depends	libgslcblas0	>=2.4
Depends	libstdc++6	>=5.2
Suggests	clonalframeml

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rendered as:

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

To install/use clonalframe @ version 1.2-9 ...

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 clonalframe=1.2-9

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

Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).

Previous Version: 1.2-9

Next Version: 1.2-9

clonalframe 1.2-9	debian/buster deb arm64 main latest 44.0 KB — 1 year, 1 month ago	4
clonalframe 1.2-9	debian/buster deb armhf main latest 40.7 KB — 1 year, 1 month ago	3
clonalframe 1.2-9	debian/buster deb arm64 main latest 44.0 KB — 1 year, 1 month ago	4

clonalframe 1.2-9

One-liner (summary)

Description

License

Size

Downloads

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This package has 13 files/directories.

clonalframe

clonalframe

clonalframe

Dependencies

Checksum (md5)