BSD Portsbiology/trimmomatic 0.39_2 FreeBSD
Flexible read trimming tool for Illumina NGS data
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv3
- Categories
- biology, java
- Package size
- 129.7 KiB, 161.5 KiB installed
Description
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/trimmomatic | 0.39_2 |
| NetBSD | biology/trimmomatic | 0.38 |
| DragonFly | biology/trimmomatic | 0.39 |
| HardenedBSD | biology/trimmomatic | 0.39_2 |
| GhostBSD | biology/trimmomatic | 0.39_2 |
Install
Binary package:
pkg install trimmomaticFrom the ports tree:
cd /usr/ports/biology/trimmomatic/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= trimmomatic>0:biology/trimmomaticPackages
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 | 0.39_2 | 0.39_2 | 0.39 | 0.39 | 0.39_2 |
| FreeBSD:14:quarterly | 0.39_2 | 0.39_2 | n/a | 0.39 | 0.39_2 |
| FreeBSD:15:latest | 0.39_2 | 0.39_2 | n/a | 0.39 | 0.39 |
| FreeBSD:15:quarterly | 0.39_2 | 0.39_2 | n/a | n/a | n/a |
| FreeBSD:16:latest | 0.39_2 | 0.39_2 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
The Makefile names none itself; they come from USES and USE_*.
The full lists below include those, and their dependencies in turn.
Run dependencies 53
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- audio/alsa-lib
- converters/libiconv
- devel/gettext-runtime
- devel/glib20
- devel/libffi
- devel/libinotify
- devel/pcre2
- devel/py-packaging
- devel/readline
- graphics/giflib
- graphics/graphite2
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/png
- graphics/tiff
- java/javavmwrapper
- java/openjdk21
- lang/python312
- lang/python315
- math/mpdecimal
- print/freetype2
- print/harfbuzz
- print/indexinfo
- textproc/expat2
- x11-fonts/dejavu
- x11-fonts/encodings
- x11-fonts/font-bh-ttf
- x11-fonts/font-misc-ethiopic
- x11-fonts/font-misc-meltho
- x11-fonts/fontconfig
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-fonts/xorg-fonts-truetype
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXtst
- x11/libxcb
- x11/xorgproto
Required by 1
Configuration
No options to configure.
- USES
- java zip
- Service scripts
- none
Message after installing
===> NOTICE: The trimmomatic 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/trimmomatic
- %%JAVAJARDIR%%/trimmomatic.jar
- share/trimmomatic/adapters/NexteraPE-PE.fa
- share/trimmomatic/adapters/TruSeq2-PE.fa
- share/trimmomatic/adapters/TruSeq2-SE.fa
- share/trimmomatic/adapters/TruSeq3-PE-2.fa
- share/trimmomatic/adapters/TruSeq3-PE.fa
- share/trimmomatic/adapters/TruSeq3-SE.fa
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| Trimmomatic-0.39.zip | 133596 | 2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca |
Master sites 1
- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
Commit history 0
No commits in the history this site was built from.