Cloudsmith - Repositories - Ultimaker (ultimaker) - debian-backup (debian-backup) - sim4db

Package Search Help

You can use boolean logic (e.g. AND/OR/NOT) for complex search queries. For more help and examples, see the search documentation.

Search by package name:
my-package _(implicit)
name:my-package _(explicit)

Search by package filename:
filename:my-package.ext

Search by package tag:
tag:latest

Search by package version:
version:1.0.0 prerelease:true _{(prereleases)}
prerelease:false _{(no prereleases)}

Search by package architecture:
architecture:x86_64

Search by package distribution:
distribution:el

Search by package license:
license:MIT

Search by package format:
format:deb

Search by package status:
status:in_progress

Search by package file checksum:
checksum:5afba

Search by package security status:
severity:critical

Search by package vulnerabilities:
vulnerabilities:>1
vulnerabilities:<1000

Search by # of package downloads:
downloads:>8
downloads:<100

Search by package type:
type:binary
type:source

Search by package size (bytes):
size:>50000
size:<10000

Search by dependency name/version:
dependency:log4j
dependency:log4j=1.0.0
dependency:log4j>1.0.0

Search by uploaded date:
uploaded:>"1 day ago"
uploaded:<"August 14, 2022 EST"

Search by entitlement token (identifier):
entitlement:3lKPVJPosCsY

Search by policy violation:
policy_violated:true
deny_policy_violated:true
license_policy_violated:true
vulnerability_policy_violated:true

Search by repository:
repository:repo-name

Search by last download date:
last_downloaded:<"30 days ago"
last_downloaded:>"August 14, 2022 EST"

Search queries for all Debian-specific (and related) package types

Search by component:
deb_component:unstable

Search queries for all Maven-specific (and related) package types

Search by group ID:
maven_group_id:org.apache

Search queries for all Docker-specific (and related) package types

Search by image digest:
docker_image_digest:sha256:7c5..6d4
(full hashref only)

Search by layer digest:
docker_layer_digest:sha256:4c4..ae4
(full hashref only)

Search queries for all Generic-specific package types

Search by file path:
generic_filepath:path/to/file.txt

Search by directory:
generic_directory:path/to

Field type modifiers (depending on the type, you can influence behaviour)

For all queries, you can use:
~foo for negation

For string queries, you can use:
^foo to anchor to start of term
foo$ to anchor to end of term
foo*bar for fuzzy matching

For number/date or version queries, you can use:
>foo for values greater than
>=foo for values greater / equal
<foo for values less than
<=foo for values less / equal

Need a secure and centralised artifact repository to deliver Alpine, Cargo, CocoaPods, Composer, Conan, Conda, CRAN, Dart, Debian, Docker, Generic, Go, Helm, Hex, HuggingFace, LuaRocks, Maven, npm, NuGet, P2, Python, RedHat, Ruby, Swift, Terraform, Vagrant, VSX, Raw & More packages?

Cloudsmith is the new standard in Package / Artifact Management and Software Distribution.

With support for all major package formats, you can trust us to manage your software supply chain.

Start My Free Trial

Set Me Up

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).

sim4db 0~20150903+r2013-6

Download

One-liner (summary)

batch spliced alignment of cDNA sequences to a target genome

Description

Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc algorithms to determine the alignments, but incorporates a fast sequence indexing and retrieval mechanism, implemented in the sister package 'leaff', to speedily process large volumes of sequences.

While sim4db produces alignments in the same way as sim4 or sim4cc, it has additional features to make it more amenable for use with whole-genome annotation pipelines. A script file can be used to group pairings between cDNAs and their corresponding genomic regions, to be aligned as one run and using the same set of parameters. Sim4db also optionally reports more than one alignment for the same cDNA within a genomic region, as long as they meet user-defined criteria such as minimum length, percentage sequence identity or coverage. This feature is instrumental in finding all alignments of a gene family at one locus. Lastly, the output is presented either as custom sim4db alignments or as GFF3 gene features.

This package is part of the Kmer suite.

License

Unknown

Size

367.5 KB

Downloads

Status	Completed
Checksum (MD5)	f1627e00571d5e91a9039bb1591d83a6
Checksum (SHA-1)	7526f946e736fab82914d70aa1ec793135c08f65
Checksum (SHA-256)	f5351f869f62fa491277342ae27647929e9577256b82e1664206955752454156
Checksum (SHA-512)	3b38a42ca38aa5deb67b56f38370fb38d29aa981eb836b127229a371d4d00cfa93…
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 ago
Uploaded By
Slug Id	sim4db_020150903r2013-6_armhfdeb-iwus
Unique Id	DOZEOuLkrwAe
Version (Raw)	0~20150903+r2013-6
Version (Parsed)	Type: Unknown
	extended metadata
Homepage	http://kmer.sourceforge.net
Installed Size	2.6 MB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science
Source	kmer

	sim4db 0~20150903+r2013-6	debian/buster deb armhf main latest 367.5 KB — 1 year ago	4

Dependencies

Checksum (md5)

0781e4563d0d991d2b7760da1e308b1b

Depends	libc6	>=2.7
Depends	libgcc1	>=1:3.5
Depends	libstdc++6	>=5.2
Recommends	kmer-examples
Recommends	leaff

Package statistics are no longer available on cloudsmith.io. Please visit our new web app to access this feature.

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

To install/use sim4db @ version 0~20150903+r2013-6 ...

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 sim4db=0~20150903+r2013-6

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

Next Version