biology/velvet 1.2.10_2 FreeBSD

Sequence assembler for very short reads

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Categories: biology
Package size: 615.8 KiB, 931.8 KiB installed

Description

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).

Citation:

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

In the other systems

The newest version among them is 1.2.10, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

FreeBSD

biology/velvet

1.2.10_2 newest

none known

[email protected]

DragonFly

biology/velvet

1.2.10_2 newest

none known

[email protected]

HardenedBSD

biology/velvet

1.2.10_2 newest

no data

[email protected]

GhostBSD

biology/velvet

1.2.10_2 newest

no data

[email protected]

Install

Binary package:

pkg install velvet

From the ports tree:

cd /usr/ports/biology/velvet/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	velvet>0:biology/velvet

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

1.2.10_2

FreeBSD:14:quarterly

1.2.10_2

n/a

1.2.10_2

FreeBSD:15:latest

1.2.10_2

n/a

1.2.10_2

FreeBSD:15:quarterly

1.2.10_2

n/a

FreeBSD:16:latest

1.2.10_2

n/a

FreeBSD:16:quarterly

n/a

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/velvet"]
  me --> d0["devel/gettext-runtime"]
  me --> d1["devel/libffi"]
  me --> d2["devel/readline"]
  me --> d3["lang/perl5.42"]
  me --> d4["lang/python312"]
  me --> d5["math/mpdecimal"]
  me --> d6["print/indexinfo"]
  me --> d7["textproc/expat2"]
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

The Makefile names none itself; they come from USES and USE_*.

The full lists below include those, and their dependencies in turn.

Build dependencies 8

Run dependencies 8

No port depends on this one.

Configuration

Options name: biology_velvet

Option

Default

Description

DOCS

off

Build and/or install documentation

USES: perl5 gmake shebangfix tar:tgz
Service scripts: none

Files

distinfo 1

File

Size

SHA256

velvet_1.2.10.tgz

1.8818559e+07

884dd488c2d12f1f89cdc530a266af5d3106965f21ab9149e8cb5c633c977640

Master sites 1

http://www.ebi.ac.uk/~zerbino/velvet/

Commit history 0

No commits in the history this site was built from.