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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).

Debian logo jellyfish-examples  2.2.10-2

One-liner (summary)

count k-mers in DNA sequences (examples for testing)

Description

JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism.

JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the "jellyfish dump" command.

This package contains examples to test the package

License

Unknown

Size

419.4 KB

Downloads

2

Status  Completed
Checksum (MD5) 6ed8af24d960beb71d5567f64c419b8c
Checksum (SHA-1) ad478681f5581cc620d886b71778f8d3191cd4d9
Checksum (SHA-256) 5e1366f01c7ef79320e28e6a69db7a2b34ad57b46fcccb55e6c43c954924ec7c
Checksum (SHA-512) 9a8f143dc022c1b95cd75e33ee4e4615896613800ba4a0cd1e98a892a8dc9a2b8d…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 11 months, 1 week ago
Uploaded By alex-borro
Slug Id jellyfish-examples_2210-2_arm64deb-hs9j
Unique Id kVD1BZ8NHi6c
Version (Raw) 2.2.10-2
Version (Parsed)
  • Major: 2
  • Minor: 2
  • Patch: 10
  • Pre (Str): (empty)
  • Pre (Num Array): 2
  • Type: SemVer (Strict)
  extended metadata
Homepage http://www.cbcb.umd.edu/software/jellyfish/
Installed Size 1.8 MB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
Source jellyfish
pkg jellyfish-examples_2.2.10-2_arm… 2
419.4 KB
md5 sha1 sha256 sha512
Package Contents (jellyfish-examples_2.2.10-2_arm64.deb)
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This package has 48 files/directories.

Dependencies

5

Checksum (md5)

1555380c7c5b27435f3e709fbfb1c09b

Depends
jellyfish
Depends
libc6 >=2.17
Depends
libgcc1 >=1:3.0
Depends
libjellyfish-2.0-2
Depends
libstdc++6 >=5.2

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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 jellyfish-examples=2.2.10-2
Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.
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