BSD Portsbiology/picard-tools 3.5.0 FreeBSD
CLI tools for manipulating high-throughput sequencing (HTS) data
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- MIT
- Categories
- biology, java
- Package size
- 57387.2 KiB, 63245.8 KiB installed
Description
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/picard-tools | 3.5.0 |
| DragonFly | biology/picard-tools | 2.22.9 |
| HardenedBSD | biology/picard-tools | 3.5.0 |
| GhostBSD | biology/picard-tools | 3.5.0 |
Install
Binary package:
pkg install picard-toolsFrom the ports tree:
cd /usr/ports/biology/picard-tools/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= picard-tools>0:biology/picard-toolsPackages
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 | 3.5.0 | 3.5.0 | 2.22.9 | - | 3.5.0 |
| FreeBSD:14:quarterly | 3.5.0 | 3.5.0 | n/a | - | 3.5.0 |
| FreeBSD:15:latest | 3.5.0 | 3.5.0 | n/a | - | 2.22.9 |
| FreeBSD:15:quarterly | 3.5.0 | 3.5.0 | n/a | n/a | n/a |
| FreeBSD:16:latest | 3.5.0 | 3.5.0 | 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 1
samtools: biology/samtools
The full lists below include those, and their dependencies in turn.
Run dependencies 61
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- audio/alsa-lib
- biology/htslib
- biology/samtools
- converters/libiconv
- devel/gettext-runtime
- devel/glib20
- devel/libffi
- devel/libinotify
- devel/libunistring
- devel/pcre2
- devel/py-packaging
- devel/readline
- dns/libidn2
- dns/libpsl
- ftp/curl
- 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
- security/libssh2
- textproc/expat2
- www/libnghttp2
- 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:run
- Service scripts
- none
- Conflicts with
- picard
Message after installing
===> NOTICE: The picard-tools 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
| File | Size | SHA256 |
|---|---|---|
| picard.jar | 6.4763062e+07 | b7d97861c3a54ba5a421f5a317f38382f955803862d30ef4aca2bcdc54943631 |
Master sites 1
- http://github.com/broadinstitute/picard/releases/download/${PORTVERSION}/