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 Open-Source — ultimaker 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).
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Debian logo cgview  0.0.20100111-4

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One-liner (summary)

Circular Genome Viewer

Description

CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature information and rendering options are supplied to the program using an XML file, a tab delimited file, or an NCBI ptt file. CGView converts the input into a graphical map (PNG, JPG, or Scalable Vector Graphics format), complete with labels, a title, legends, and footnotes. In addition to the default full view map, the program can generate a series of hyperlinked maps showing expanded views. The linked maps can be explored using any web browser, allowing rapid genome browsing, and facilitating data sharing. The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases.

In addition to the CGView application, an API is available for generating maps from within other Java applications, using the cgview package.

CGView can be used for any of the following: * Bacterial genome visualization and browsing - CGView can be incorporated into bacterial genome annotation pipelines, as a means of generating web content for data visualization and navigation. The PNG and image map content does not require Java applets or special browser plugins. * Genome poster generation - CGView can generate poster-sized images of circular genomes in rasterized image formats or in Scalable Vector Graphics format. * Sequence analysis visualization - CGView can be used to display the output of sequence analysis programs in a circular context.

CGView features: * Images can be generated in PNG, JPG, or SVG format. See the CGView gallery. * Static or interactive maps can be generated. The interactive maps make use of standard PNG images and HTML image maps. Scalable Vector Graphics output is included in the interactive maps (see example). * The XML input allows complete control over the appearance of the map. * Tab delimited input files and NCBI ptt files can be used as an alternative to the XML format. * The CGView API can be used to incorporate CGView into Java applications. * The CGView applet can be used to incorporate zoomable maps into web pages (see example). * The CGView Server can be used to generate maps online.

License

Unknown

Size

574.3 KB

Downloads

1

Tags

debian/buster deb armhf main latest

Status  Completed
Checksum (MD5) 831cf3491e5ffc74d93c65998ad3db47
Checksum (SHA-1) b0736d1c7807105e6f0897dcd512d0872deb0807
Checksum (SHA-256) a983a2ff7d7b2646e9ba1855f23fa2e65a6f38d07831f3cf20e8e0264abb3c74
Checksum (SHA-512) 3a5993ad57aebb30dd4bc132c897172d18b4bc3444024c0d25693e43a646850dc8…
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 10 months, 1 week ago
Uploaded By alex-borro
Slug Id cgview_0020100111-4_armhfdeb-tovt
Unique Id sCFoi0ykSh7H
Version (Raw) 0.0.20100111-4
Version (Parsed)
  • Major: 0
  • Minor: 0
  • Patch: 20100111
  • Pre (Str): (empty)
  • Pre (Num Array): 4
  • Type: SemVer (Strict)
  extended metadata
Homepage http://wishart.biology.ualberta.ca/cgview/
Installed Size 625.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg cgview_0.0.20100111-4_armhf.deb 1
574.3 KB 		md5 sha1 sha256 sha512
Package Contents (cgview_0.0.20100111-4_armhf.deb)
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This package has 25 files/directories.

Dependencies

8

Checksum (md5)

3190e8d1b4125b59f5bc9d42ef922c50

Depends
default-jre
Depends
java10-runtime
Depends
java11-runtime
Depends
jarwrapper >=0.5
Depends
libbatik-java
Depends
libcommons-lang-java
Depends
libjargs-java
Depends
libxerces2-java
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rendered as: Latest version of 'cgview' @ Cloudsmith

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

To install/use cgview @ version 0.0.20100111-4 ...

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 cgview=0.0.20100111-4
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).
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