| Port details |
- py-loompy Work with .loom files for single-cell RNA-seq data
- 3.0.6 biology
 =0      3.0.6Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-09-21 08:05:03
- Last Update: 2021-04-07 08:09:01
- Commit Hash: cf118cc
- Also Listed In: python
- License: BSD2CLAUSE
- Description:
- Loom is an efficient file format for large omics datasets. Loom files contain
a main matrix, optional additional layers, a variable number of row and column
annotations, and sparse graph objects. Under the hood, Loom files are HDF5 and
can be opened from many programming languages, including Python, R, C, C++,
Java, MATLAB, Mathematica, and Julia.
Key features:
* Single file that can be moved around
* Metadata travels with the main data
* Data, clustering, layout, annotation stored together
* Efficient random access
* Automatic, on-the-fly compression
* Out-of-memory data processing
* Open source, BSD license
WWW: https://loompy.org/
- SVNWeb : git : Homepage
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}loompy>0:biology/py-loompy@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-loompy/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-loompy
- pkg install py38-loompy
NOTE: This is a Python port. Instead of py38-loompy listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py38-loompy
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1592273431
SHA256 (loompy-3.0.6.tar.gz) = 58e9763b8ab1af2a4a0e3805d120458b5184fd2b0f3031657ecce33c63ca4c46
SIZE (loompy-3.0.6.tar.gz) = 41108
- 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<1.20,1 : math/py-numpy@py38
- py38-h5py>0 : science/py-h5py@py38
- py38-pandas>0 : math/py-pandas@py38
- py38-scipy>0 : science/py-scipy@py38
- py38-setuptools>0 : devel/py-setuptools@py38
- python3.8 : lang/python38
- This port is required by:
- for Run
-
- biology/py-orange3-single-cell
- Configuration Options:
- No options to configure
- Options name:
- biology_py-loompy
- USES:
- python:3.7+
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 10
| Commit History - (may be incomplete: see SVNWeb link above for full details) |
| Date | By | Description |
|---|
07 Apr 2021 08:09:01
  3.0.6
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
06 Apr 2021 14:31:07
3.0.6
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
30 Jan 2021 13:29:58
  3.0.6
|
sunpoet |
Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
PR: 250103 |
16 Jun 2020 02:26:08
3.0.6
|
yuri |
biology/py-loompy: Update 2.0.17 -> 3.0.6 |
26 Jul 2019 20:46:57
2.0.17_1
|
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 |
02 Feb 2019 21:38:49
2.0.17
|
yuri |
biology/py-loompy: Update 2.0.16 -> 2.0.17
Reported by: portscout |
12 Dec 2018 01:35:36
2.0.16_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 |
30 Oct 2018 05:57:44
2.0.16
|
yuri |
biology/py-loompy: Update 2.0.15 -> 2.0.16
Reported by: portscout |
19 Oct 2018 05:01:45
2.0.15
|
yuri |
biology/py-loompy: Update 2.0.14 -> 2.0.15
Reported by: portscout |
21 Sep 2018 08:04:50
2.0.14
|
yuri |
New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data |
Number of commits found: 10
|
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