biology/mca-calling 0.1.0 FreeBSD

Core tools for Mosaic Chromosomal Alteration event calling

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-08
Commit: 2414383046
License: BSD2CLAUSE
Categories: biology
Package size: 1.7 KiB, 0.2 KiB installed

Description

The mca-calling meta-port provides the core tools needed for performing a typical mCA (Mosaic Chromosomal Alteration) analysis, including conversion of SRA VCF files to a format suitable for haplohseq and MoCha, and haplohseq and MoCha event calling. The GWAS analysis that follows is typically done with R-based tools installed within R.

In the other systems

System

Port

Version

FreeBSD

biology/mca-calling

0.1.0

HardenedBSD

biology/mca-calling

0.1.0

GhostBSD

biology/mca-calling

0.1.0

Install

Binary package:

pkg install mca-calling

From the ports tree:

cd /usr/ports/biology/mca-calling/ && make install clean

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

RUN_DEPENDS=	mca-calling>0:biology/mca-calling

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	0.1.0	0.1.0	-	-	-
FreeBSD:14:quarterly	0.1.0	0.1.0	n/a	-	-
FreeBSD:15:latest	0.1.0	0.1.0	n/a	-	-
FreeBSD:15:quarterly	0.1.0	0.1.0	n/a	n/a	n/a
FreeBSD:16:latest	0.1.0	0.1.0	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependencies

As this port's Makefile names them.

Runtime 12

sra-tools>0 : biology/sra-tools
bcftools>0 : biology/bcftools
samtools>0 : biology/samtools
vcf-split>0 : biology/vcf-split
ad2vcf>0 : biology/ad2vcf
vcf2hap>0 : biology/vcf2hap
haplohseq>0 : biology/haplohseq
bio-mocha>0 : biology/bio-mocha
bedtools>0 : biology/bedtools
mawk>0 : lang/mawk
curl>0 : ftp/curl
liblz4>0 : archivers/liblz4

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

Run dependencies 121

The first 100 are listed.

No port depends on this one.

Configuration

No options to configure.

USES: metaport
Service scripts: none

Message after installing

===>   NOTICE:

The mca-calling port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

No file lists for this port.

Commit history 1

Date Commit Credits Log message

2026-10-08

2414383046

Jason W. Bacon

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.