BSD Ports

biology/haplohseq 0.1.2.3_4 FreeBSD

Identify regions of allelic imbalance

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
MIT
Categories
biology
Package size
8827.4 KiB, 61737.5 KiB installed

Description

Haplohseq identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample. Input to the software includes a VCF file of genotypes and estimated phased genotypes.

In the other systems

SystemPortVersion
FreeBSDbiology/haplohseq0.1.2.3_4
NetBSDwip/haplohseq0.1.2.5
HardenedBSDbiology/haplohseq0.1.2.3_4
GhostBSDbiology/haplohseq0.1.2.3_3

Install

Binary package:

pkg install haplohseq

From the ports tree:

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

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

RUN_DEPENDS=	haplohseq>0:biology/haplohseq

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:latest0.1.2.3_40.1.2.3_4-0.1.2.3_10.1.2.3_4
FreeBSD:14:quarterly0.1.2.3_40.1.2.3_4n/a0.1.2.3_10.1.2.3_4
FreeBSD:15:latest0.1.2.3_40.1.2.3_4n/a0.1.2.3_10.1.2.3_1
FreeBSD:15:quarterly0.1.2.3_40.1.2.3_4n/an/an/a
FreeBSD:16:latest0.1.2.3_40.1.2.3_4n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Library 1

Runtime 1

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

Build dependencies 12
Run dependencies 89
Required by 1

Configuration

Options name: biology_haplohseq

OptionDefaultDescription
EXAMPLESoffBuild and/or install examples
USES
compiler:c++14-lang gmake localbase:ldflags python
Service scripts
none

Message after installing

===>   NOTICE:

The haplohseq 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

pkg-plist 8
  • bin/haplohseq
  • bin/haplohseq-example
  • share/examples/haplohseq/example/example_input/tumor_exome.vcf
  • share/examples/haplohseq/example/example_run.sh
  • share/examples/haplohseq/ldmap/hg19.exome.ldmap
  • share/examples/haplohseq/scripts/haplohseq_plot.R
  • share/examples/haplohseq/scripts/ldmap.py
  • share/examples/haplohseq/scripts/simple_phaser.py
distinfo 1
FileSizeSHA256
outpaddling-haplohseq-0.1.2-3-gfeb9267_GH0.tar.gz1.2085111e+07a23691f16f1c03e0dfd833896068e05eaa139d488a7094a49033aeacba948cb1

Commit history 3

DateCommitCreditsLog message
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.
97a84ef467 Dima Panov */*: update boost consumers after boost-1.92
213840c151 Dima Panov */*: bump consumers after devel/boost update