BSD Ports

biology/py-crossmap 0.7.4 FreeBSD

Lift over genomics coordinates between assemblies

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
GPLv3+
Categories
biology, python
Package size
76.3 KiB, 482.3 KiB installed

Description

CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.

In the other systems

SystemPortVersion
FreeBSDbiology/py-crossmap0.7.4
DragonFlybiology/py-crossmap0.7.3_1
HardenedBSDbiology/py-crossmap0.7.4
GhostBSDbiology/py-crossmap0.7.4

Install

Binary package:

pkg install py312-crossmap

From the ports tree:

cd /usr/ports/biology/py-crossmap/ && make install clean

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

RUN_DEPENDS=	py312-crossmap>0:biology/py-crossmap

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:latest0.7.40.7.4--0.7.4
FreeBSD:14:quarterly0.7.40.7.4n/a-0.7.4
FreeBSD:15:latest0.7.40.7.4n/a-0.7.3_1
FreeBSD:15:quarterly0.7.40.7.4n/an/an/a
FreeBSD:16:latest0.7.40.7.4n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Runtime 3

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

Build dependencies 13
Run dependencies 36
Required by 1

Configuration

No options to configure.

USES
python
Service scripts
none

Message after installing

===>   NOTICE:

The py312-crossmap 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

distinfo 1
FileSizeSHA256
crossmap-0.7.4.tar.gz32919f4ff313ecb9f5ad646c515e46e3811147a575c2f934893924ee376cef2e024b5
Master sites 1
  • PYPI

Commit history 2

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.
e92bdc925e Jason W. Bacon biology/py-crossmap: Update to 0.7.4
A few fixes and modernizations Changes: https://github.com/liguowang/CrossMap/releases Reported by: portscout