| Port details |
- groopm Metagenomic binning suite
- 0.3.4_3 biology
 =0      0.3.4_3Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-12-07 00:10:56
- Last Update: 2022-03-25 13:38:04
- Commit Hash: dab6c99
- Also Listed In: python
- License: GPLv3
- 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.
WWW: http://ecogenomics.github.io/GroopM/
- SVNWeb : git : Homepage
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/groopm/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/groopm
- pkg install GroopM
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: GroopM
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1544140602
SHA256 (GroopM-0.3.4.tar.gz) = 48bdaeb9010e7d81785697a55edc394ef36c2646b310d625a24bec740f1b6080
SIZE (GroopM-0.3.4.tar.gz) = 127707
- Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py38-setuptools>0 : devel/py-setuptools@py38
- python3.8 : lang/python38
- Runtime dependencies:
-
- py38-numpy>=1.16,1<1.21,1 : math/py-numpy@py38
- py38-matplotlib>=1.1.0 : math/py-matplotlib@py38
- py38-scipy>=0.10.1 : science/py-scipy@py38
- py38-tables>=2.3 : devel/py-tables@py38
- py38-setuptools>0 : devel/py-setuptools@py38
- python3.8 : lang/python38
- There are no ports dependent upon this port
- Configuration Options:
- No options to configure
- Options name:
- biology_groopm
- USES:
- python:3.7+
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: see SVNWeb link above for full details) |
| Date | By | Description |
|---|
25 Mar 2022 13:38:04
  0.3.4_3
|
Po-Chuan Hsieh (sunpoet) |
biology/groopm: Fix build with setuptools 58.0.0+
With hat: python |
10 May 2021 20:13:20
0.3.4_3
|
Thierry Thomas (thierry) |
math/py-matplotlib: chase minimum Python version in dependent ports
Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.
PR: 255347
Reported by: sunpoet |
07 Apr 2021 08:09:01
0.3.4_3
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
06 Apr 2021 14:31:07
0.3.4_3
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
24 Dec 2020 09:03:39
  0.3.4_3
|
antoine |
scipy 1.5.4 is only compatible with python 3.6+
Reported by: pkg-fallout |
13 Aug 2020 19:19:24
0.3.4_3
|
yuri |
biology/groopm: Remove python's 2.7 restriction placed here by mistake |
23 Feb 2020 15:25:53
0.3.4_2
|
antoine |
Deprecate a few ports
With hat: portmgr |
26 Jul 2019 20:46:57
0.3.4_2
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.
PR: 238330 |
07 Jan 2019 09:44:42
0.3.4_1
|
antoine |
biology/groopm fails to build with python3
PR: 234633 |
12 Dec 2018 01:35:36
0.3.4_1
|
gerald |
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using Mk/bsd.octave.mk which in turn features USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.
PR: 231590 |
07 Dec 2018 00:10:06
0.3.4
|
yuri |
New port: math/groopm: Metagenomic binning suite |
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