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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).

dazzdb 1.0+git20180908.0bd5e07-1

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One-liner (summary)

manage nucleotide sequencing read data

Description

To facilitate the multiple phases of the dazzler assembler, all the read data is organized into what is effectively a database of the reads and their meta-information. The design goals for this data base are as follows: * The database stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files. This avoids duplicating the same data, once in the source file and once in the database. * The data base can be built up incrementally, that is new sequence data can be added to the data base over time. * The data base flexibly allows one to store any meta-data desired for reads. This is accomplished with the concept of *tracks* that implementors can add as they need them. * The data is held in a compressed form equivalent to the .dexta and .dexqv files of the data extraction module. Both the .fasta and .quiva information for each read is held in the data base and can be recreated from it. The .quiva information can be added separately and later on if desired. * To facilitate job parallel, cluster operation of the phases of the assembler, the database has a concept of a *current partitioning* in which all the reads that are over a given length and optionally unique to a well, are divided up into *blocks* containing roughly a given number of bases, except possibly the last block which may have a short count. Often programs can be run on blocks or pairs of blocks and each such job is reasonably well balanced as the blocks are all the same size. One must be careful about changing the partition during an assembly as doing so can void the structural validity of any interim block-based results.

License

Unknown

Size

149.6 KB

Downloads

Status	Completed
Checksum (MD5)	56a3611c511bde7c6c848cda9650a6cf
Checksum (SHA-1)	51c416cdb923a0e1279d0048f65fe707e8e2111c
Checksum (SHA-256)	d949539ea34d7a8329292f8e640edc586904f849a6a0bf35d2c9b1398c4d5e60
Checksum (SHA-512)	ea1a6993cc7bfdb27b07bc3008c3b55283397d0995f5ed70384944909542531868…
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, 3 weeks ago
Uploaded By
Slug Id	dazzdb_10git201809080bd5e07-1_arm64deb-pihq
Unique Id	GIBc6bjE7dIE
Version (Raw)	1.0+git20180908.0bd5e07-1
Version (Parsed)	Major: 1 Minor: 0 Type: SemVer (Compat) Metadata: git20180908.0bd5e07-1
	extended metadata
Homepage	https://github.com/thegenemyers/DAZZ_DB
Installed Size	1.4 MB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

d35722a2ba5bff8304fda6690ca165d8

Depends	libc6	>=2.17
Depends	zlib1g	>=1:1.1.4

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 'dazzdb' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 'dazzdb' @ Cloudsmith|
.. |This version of 'dazzdb' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 'dazzdb' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/1.0+git20180908.0bd5e07-1/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'dazzdb' @ Cloudsmith" /></a>

rendered as:

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

[![Latest version of 'dazzdb' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/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/dazzdb/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 'dazzdb' @ Cloudsmith|
.. |Latest version of 'dazzdb' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/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/dazzdb/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/dazzdb/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/dazzdb/latest/a=arm64;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 'dazzdb' @ Cloudsmith"]

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

rendered as:

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

To install/use dazzdb @ version 1.0+git20180908.0bd5e07-1 ...

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 dazzdb=1.0+git20180908.0bd5e07-1

Warning: Note that this package is for Debian 10 (Buster) / arm64 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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