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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).

ea-utils 1.1.2+dfsg-5

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One-liner (summary)

command-line tools for processing biological sequencing data

Description

Ea-utils provides a set of command-line tools for processing biological sequencing data, barcode demultiplexing, adapter trimming, etc.

Primarily written to support an Illumina based pipeline - but should work with any FASTQs.

Main Tools are:

* fastq-mcf Scans a sequence file for adapters, and, based on a log-scaled threshold, determines a set of clipping parameters and performs clipping. Also does skewing detection and quality filtering. * fastq-multx Demultiplexes a fastq. Capable of auto-determining barcode id's based on a master set fields. Keeps multiple reads in-sync during demultiplexing. Can verify that the reads are in-sync as well, and fail if they're not. * fastq-join Similar to audy's stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same "squared distance for anchored alignment" as other tools. * varcall Takes a pileup and calculates variants in a more easily parameterized manner than some other tools.

License

Unknown

Size

150.1 KB

Downloads

Status	Completed
Checksum (MD5)	eb53092faca34bf3e95e3bf185f5ea86
Checksum (SHA-1)	7c1398fe40c49637dd626eef32e2118b39933445
Checksum (SHA-256)	d7a2e877f58b61307487b139ea980683e4f38a4e1aa28076769a75f482070c7f
Checksum (SHA-512)	3909e02925e1e33ad2f85e282f21399044df41bb37a00ae4a1bd9b3fc27c9bbe8d…
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	8 months, 1 week ago
Uploaded By
Slug Id	ea-utils_112dfsg-5_armhfdeb-hzmb
Unique Id	espcoKNpsfvX
Version (Raw)	1.1.2+dfsg-5
Version (Parsed)	Major: 1 Minor: 1 Patch: 2 Type: SemVer (Strict) Metadata: dfsg-5
	extended metadata
Homepage	https://expressionanalysis.github.io/ea-utils/
Installed Size	408.0 KB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

cdc82b052ed51814382ed3eb8f7eaa6f

Depends	libc6	>=2.15
Depends	libgcc1	>=1:3.5
Depends	libgsl23
Depends	libgslcblas0
Depends	libstdc++6	>=5.2
Depends	r-base-core
Depends	r-cran-formula
Depends	r-cran-getopt
Depends	r-cran-ggplot2
Depends	r-cran-hmisc
Depends	r-cran-lattice
Depends	r-cran-survival
Depends	zlib1g	>=1:1.2.3.3
Recommends	med-config	>=2.1

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<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/ea-utils/1.1.2+dfsg-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/ea-utils/1.1.2+dfsg-5/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'ea-utils' @ Cloudsmith" /></a>

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

To install/use ea-utils @ version 1.1.2+dfsg-5 ...

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 ea-utils=1.1.2+dfsg-5

Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.

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