BSD Portsbiology/bio-mocha 1.22 FreeBSD
Bcftools plugin for mosaic chromosomal alteration analysis
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MIT
- Categories
- biology
- Package size
- 84.2 KiB, 247.1 KiB installed
Description
MoChA is a bcftools plugin released under the MIT license for mosaic chromosomal alteration detection and analysis from DNA microarray or whole genome sequence data. It can be used both with Illumina and Affymetrix data. It can also be used for detection of germline copy number variants. Data can be prepared in usable file formats using the gtc2vcf plugin.
In the other systems
The newest version among them is 1.22, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| FreeBSD | biology/bio-mocha | 1.22 newest | none known | - | [email protected] | 2026-10-08 |
| NetBSD | biology/bio-mocha | 1.20 behind since 2026-08-31 | none known | - | [email protected] | - |
| DragonFly | biology/bio-mocha | 1.20 behind since 2026-08-31 | none known | - | [email protected] | - |
| HardenedBSD | biology/bio-mocha | 1.22 newest | no data | - | [email protected] | - |
| GhostBSD | biology/bio-mocha | 1.22 newest | no data | - | [email protected] | - |
Version history 1
Upstream's version as each commit to the port's Makefile set it, or as this site first saw it in the system's packages; the tree's own revisions are not versions here.
Install
Binary package:
pkg install bio-mochaFrom the ports tree:
cd /usr/ports/biology/bio-mocha/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= bio-mocha>0:biology/bio-mochaPackages
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 | 1.22 | 1.22 | 1.16 | - | 1.22 |
| FreeBSD:14:quarterly | 1.22 | 1.22 | n/a | - | 1.22 |
| FreeBSD:15:latest | 1.22 | 1.22 | n/a | - | 1.20_1 |
| FreeBSD:15:quarterly | 1.22 | 1.22 | n/a | n/a | n/a |
| FreeBSD:16:latest | 1.22 | 1.22 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | 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.
Dependencies
As this port's Makefile names them.
Build 2
bash: shells/bashhtslib>=1.24: biology/htslib
Library 1
libhts.so: biology/htslib
Runtime 1
bcftools>=${PORTVERSION}: biology/bcftools
The full lists below include those, and their dependencies in turn.
Build dependencies 20
Run dependencies 17
Required by 1
Configuration
No options to configure.
- USES
- autoreconf gmake localbase perl5 python:env shebangfix
- Service scripts
- none
Message after installing
===> NOTICE: The bio-mocha 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 6
- libexec/bcftools/extendFMT.so
- libexec/bcftools/mocha.so
- libexec/bcftools/mochatools.so
- share/bio-mocha/mocha_plot.R
- share/bio-mocha/pileup_plot.R
- share/bio-mocha/summary_plot.R
distinfo 2
| File | Size | SHA256 |
|---|---|---|
| bio-mocha_1.22-20250819.tar.gz | 67361 | c5d4da549e710377335b17d5222c1253152b4b4b17b5b1dfef558debe3618c8e |
| samtools-bcftools-1.22-1.24_GH0.tar.gz | 3.800098e+06 | 386ac0d2fa51da312d01aada488ec98cf44ea4bac00d2a6c6d4993291b2f8e8c |
Master sites 1
- https://software.broadinstitute.org/software/mocha/