BSD Portsbiology/groopm 0.3.4_8 FreeBSD
Metagenomic binning suite
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- GPLv3
- Categories
- biology, python
- Package size
- 277.5 KiB, 1706.4 KiB installed
Description
GroopM is a metagenomic binning toolset. It leverages spatio-temoral dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets.
GroopM is largely parameter-free. Use: groopm -h for more info.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/groopm | 0.3.4_8 |
| HardenedBSD | biology/groopm | 0.3.4_8 |
| GhostBSD | biology/groopm | 0.3.4_8 |
Install
Binary package:
pkg install GroopMFrom the ports tree:
cd /usr/ports/biology/groopm/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= GroopM>0:biology/groopmPackages
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 | 0.3.4_8 | 0.3.4_8 | - | 0.3.4_5 | 0.3.4_8 |
| FreeBSD:14:quarterly | 0.3.4_8 | 0.3.4_8 | n/a | 0.3.4_5 | 0.3.4_8 |
| FreeBSD:15:latest | 0.3.4_8 | 0.3.4_8 | n/a | 0.3.4_5 | 0.3.4_5 |
| FreeBSD:15:quarterly | 0.3.4_8 | 0.3.4_8 | n/a | n/a | n/a |
| FreeBSD:16:latest | 0.3.4_8 | 0.3.4_8 | 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 4
${PYTHON_PKGNAMEPREFIX}numpy>=1.16: math/py-numpy${PYTHON_PKGNAMEPREFIX}matplotlib>=1.1.0: math/py-matplotlib${PYTHON_PKGNAMEPREFIX}scipy>=0.10.1: science/py-scipy${PYTHON_PKGNAMEPREFIX}tables>=2.3: devel/py-tables
The full lists below include those, and their dependencies in turn.
Build dependencies 11
Run dependencies 89
- archivers/brotli
- archivers/c-blosc2
- archivers/libdeflate
- archivers/liblz4
- archivers/lzo2
- archivers/py-brotli
- archivers/py-zopfli
- archivers/ucl
- archivers/zopfli
- archivers/zstd
- converters/fribidi
- converters/libiconv
- devel/binutils
- devel/gettext-runtime
- devel/glib20
- devel/libffi
- devel/libinotify
- devel/pcre2
- devel/py-cycler
- devel/py-lxml
- devel/py-mock
- devel/py-olefile
- devel/py-packaging
- devel/py-pyparsing
- devel/py-python-dateutil
- devel/py-six
- devel/py-tables
- devel/py-unicodedata2
- devel/readline
- graphics/gdk-pixbuf2
- graphics/giflib
- graphics/graphite2
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/libavif
- graphics/libimagequant
- graphics/libyuv
- graphics/openjpeg
- graphics/png
- graphics/py-pillow
- graphics/tiff
- graphics/webp
- lang/gcc14
- lang/python312
- lang/python315
- lang/tcl86
- math/gmp
- math/mpc
- math/mpdecimal
- math/mpfr
- math/openblas
- math/py-contourpy
- math/py-kiwisolver
- math/py-matplotlib
- math/py-numexpr
- math/py-numpy
- math/qhull
- misc/shared-mime-info
- multimedia/aom
- multimedia/dav1d
- multimedia/vmaf
- print/freetype2
- print/harfbuzz
- print/indexinfo
- print/libraqm
- print/py-fonttools
- science/hdf5
- science/libaec
- science/py-scipy
- security/libgcrypt
- security/libgpg-error
- sysutils/py-py-cpuinfo2
- textproc/expat2
- textproc/libxml2
- textproc/libxslt
- x11-fonts/fontconfig
- x11-fonts/libXft
- x11-toolkits/py-tkinter
- x11-toolkits/tk86
- x11/libX11
- x11/libXScrnSaver
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXrender
- x11/libxcb
- x11/xorgproto
No port depends on this one.
Configuration
No options to configure.
- USES
- python
- Service scripts
- none
Files
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| GroopM-0.3.4.tar.gz | 127707 | 48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080 |
Master sites 1
- PYPI
Commit history 0
No commits in the history this site was built from.