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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).

pilon 1.23+dfsg-1

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One-liner (summary)

automated genome assembly improvement and variant detection tool

Description

Pilon is a software tool which can be used to: * Automatically improve draft assemblies * Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including: * Single base differences * Small indels * Larger indel or block substitution events * Gap filling * Identification of local misassemblies, including optional opening of new gaps

License

Unknown

Size

411.3 KB

Downloads

Status	Completed
Checksum (MD5)	7028e62efe475f10fd1461ec092fa018
Checksum (SHA-1)	48c79a722d5cc591ec02bec651d75732918831ea
Checksum (SHA-256)	028394c5eff31e86d200d1b0c4b9f140572fdacfa42a26f48fb45af7103ee841
Checksum (SHA-512)	cb4c45125950973952b72ba1b990ea8bb7808777bf2c03db30a541148afd90ccde…
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	9 months, 4 weeks ago
Uploaded By
Slug Id	pilon_123dfsg-1_alldeb-5cqz
Unique Id	e5c6trFLey6A
Version (Raw)	1.23+dfsg-1
Version (Parsed)	Major: 1 Minor: 23 Type: SemVer (Compat) Metadata: dfsg-1
	extended metadata
Homepage	https://github.com/broadinstitute/pilon/wiki
Installed Size	480.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

0ba7b3e77d1bce289335effc05880946

Depends	default-jre
Depends	java-runtime
Depends	java-wrappers
Depends	libcommons-lang-java
Depends	libhtsjdk-java
Depends	scala-library
Replaces	pilon-non-free
Conflicts	pilon-non-free

You can embed a badge in another website that shows this or the latest version of this package.

To embed the badge for this specific package version, use the following:

[![This version of 'pilon' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'pilon' @ Cloudsmith|
.. |This version of 'pilon' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'pilon' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/pilon/1.23+dfsg-1/a=all;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'pilon' @ Cloudsmith" /></a>

rendered as:

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

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

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

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

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

rendered as:

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

To install/use pilon @ version 1.23+dfsg-1 ...

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 pilon=1.23+dfsg-1

Warning: Note that this package is for Debian 10 (Buster) / all 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).

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