BSD Ports

biology/coverm 0.8.0_3 FreeBSD

Read coverage calculator for metagenomics

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
9c878207a1
License
AGPLv3
Categories
biology

Description

CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications.

CoverM calculates coverage of genomes/MAGs `coverm genome` or individual contigs `coverm contig`. Calculating coverage by read mapping, its input can either be BAM files sorted by reference, or raw reads and reference genomes in various formats.

In the other systems

SystemPortVersion
FreeBSDbiology/coverm0.8.0_3
HardenedBSDbiology/coverm0.8.0_2
GhostBSDbiology/coverm0.8.0_2

Install

Binary package:

pkg install coverm

From the ports tree:

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

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

RUN_DEPENDS=	coverm>0:biology/coverm

Packages

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

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest-0.8.0_3---
FreeBSD:14:quarterly-0.8.0_2n/a--
FreeBSD:15:latest-0.8.0_3n/a--
FreeBSD:15:quarterly-0.8.0_2n/an/an/a
FreeBSD:16:latest-0.8.0_3n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

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 19

No port depends on this one.

Configuration

No options to configure.

USES
cargo
Service scripts
none

Files

distinfo 253
FileSizeSHA256
rust/crates/addr2line-0.25.1.crate431341b5d307320b3181d6d7954e663bd7c774a838b8220fe0593c86d9fb09f498b4b
rust/crates/adler2-2.0.1.crate13366320119579fcad9c21884f5c4861d16174d0e06250625266f50fe6898340abefa
rust/crates/aho-corasick-1.1.4.crate184015ddd31a130427c27518df266943a5308ed92d4b226cc639f5a8f1002816174301
rust/crates/ansi_term-0.12.1.crate24838d52a9bb7ec0cf484c551830a7ce27bd20d67eac647e1befb56b0be4ee39a55d2
rust/crates/anstream-1.0.0.crate28916824a212faf96e9acacdbd09febd34438f8f711fb84e09a8916013cd7815ca28d
rust/crates/anstyle-1.0.14.crate17787940b3a0ca603d1eade50a4846a2afffd5ef57a9feac2c0e2ec2e14f9ead76000
rust/crates/anstyle-parse-1.0.0.crate2204252ce7f38b242319f7cabaa6813055467063ecdc9d355bbb4ce0c68908cd8130e
rust/crates/anstyle-query-1.1.5.crate1026440c48f72fd53cd289104fc64099abca73db4166ad86ea0b4341abe65af83dadc
rust/crates/anstyle-wincon-3.0.11.crate12638291e6a250ff86cd4a820112fb8898808a366d8f9f58ce16d1f538353ad55747d
rust/crates/anyhow-1.0.103.crate487462a4385e2e34eb35d6b3efe798b9eb88096925d87726c0798709bf56d9ed84af3
rust/crates/approx-0.5.1.crate15100cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6
rust/crates/assert_cli-0.6.3.crate18660a29ab7c0ed62970beb0534d637a8688842506d0ff9157de83286dacd065c8149
rust/crates/autocfg-1.5.1.crate18911f2032f911046de80f0a198e0901378627c33f59ea0ac00e363d481118bd70a53
rust/crates/backtrace-0.3.76.crate89458bb531853791a215d7c62a30daf0dde835f381ab5de4589cfe7c649d2cbe92bd6
rust/crates/bincode-1.3.3.crate28958b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad
rust/crates/bio-2.0.3.crate199967d563b9298d39b3bdb5c45f6e91e0bdcb18d67e6d8fa034a733b7283f2db5ed29
rust/crates/bio-types-1.0.4.crate24109f4dcf54f8b7f51450207d54780bab09c05f30b8b0caa991545082842e466ad7e
rust/crates/bird_tool_utils-0.5.2.crate124007ccd842327813009703c20cd8180fa7d767a5be7a992b4182be71dbd853738c4
rust/crates/bird_tool_utils-man-0.4.0.crate16575a263d1717fd146db3c9bfc0668f9bf19d9078a79fa2c1ba54f00b6d8702d4e0b
rust/crates/bit-set-0.8.0.crate1628908807e080ed7f9d5433fa9b275196cfc35414f66a0c79d864dc51a0d825231a3

Commit history 4

DateCommitCreditsLog message
9c878207a1 Mikael Urankar lang/rust: Bump revisions after 1.99.0
PR: 299016
7316461925 Mikael Urankar lang/rust: Bump revisions after 1.98.1
PR: 298139
9c892d2601 Mikael Urankar lang/rust: Bump revisions after 1.97.1
PR: 296645
c22bd47a8e Yuri Victorovich biology/coverm: update 0.7.0 → 0.8.0