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Port details
py-bx-python Python module for reading, manipulating and writing genomic data sets
0.8.11.6 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.8.11.6Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-05-06 06:28:34
Last Update: 2021-08-17 19:10:45
Commit Hash: 640855add
Also Listed In: python
License: MIT
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}bx-python>0:biology/py-bx-python@${PY_FLAVOR}
To install the port: cd /usr/ports/biology/py-bx-python/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-bx-python
  • pkg install py38-bx-python
NOTE: This is a Python port. Instead of py38-bx-python listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py38-bx-python
Package flavors (<flavor>: <package>)
  • py38: py38-bx-python
distinfo:
Packages (timestamps in pop-ups are UTC):
py27-bx-python
ABIlatestquarterly
FreeBSD:11:aarch640.8.20.8.9
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch640.8.2-
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py36-bx-python
ABIlatestquarterly
FreeBSD:11:aarch640.8.2-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch640.8.2-
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py37-bx-python
ABIlatestquarterly
FreeBSD:11:aarch64-0.8.9
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-0.8.10
FreeBSD:13:aarch640.8.9-
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc640.8.10-
 
py38-bx-python
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.8.11.60.8.10
FreeBSD:11:armv6--
FreeBSD:11:i3860.8.11.60.8.10
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.8.11.6
FreeBSD:12:amd640.8.11.60.8.11.6
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.8.11.60.8.11.6
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-0.8.11.6
FreeBSD:13:amd640.8.11.60.8.11.6
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.8.11.60.8.11.6
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch640.8.11.6-
FreeBSD:14:amd640.8.11.6-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.8.11.6-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py38-numpy>=1.16,1<1.20,1 : math/py-numpy@py38
  2. cython-3.8 : lang/cython@py38
  3. py38-setuptools>0 : devel/py-setuptools@py38
  4. python3.8 : lang/python38
Runtime dependencies:
  1. py38-numpy>=1.16,1<1.20,1 : math/py-numpy@py38
  2. py38-setuptools>0 : devel/py-setuptools@py38
  3. python3.8 : lang/python38
This port is required by:
for Run
  1. biology/py-crossmap

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/bxlab/bx-python/tar.gz/v0.8.11-6-gbd714e3?dummy=/
Collapse this list.

Number of commits found: 16

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
17 Aug 2021 19:10:45
 files touched by this commit commit hash:640855add1423c3ab2f9bec57f84514b260702c9  0.8.11.6
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.10 -> 0.8.11-6
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.8.10
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
27 Feb 2021 03:55:36
Original commit files touched by this commit Revision:566662  0.8.10
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.9 -> 0.8.10
28 Dec 2020 23:02:15
Original commit files touched by this commit Revision:559531  0.8.9
antoine search for other commits by this committer
Drop python 2.7 support from a few ports

With hat:	portmgr
26 Jun 2020 04:17:12
Original commit files touched by this commit Revision:540420  0.8.9
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.8 -> 0.8.9

Reported by:	portscout
15 Feb 2020 20:08:30
Original commit files touched by this commit Revision:526239  0.8.8
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.6 -> 0.8.8

Reported by:	portscout
23 Nov 2019 05:53:50
Original commit files touched by this commit Revision:518184  0.8.6
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.4 -> 0.8.6

Reported by:	portscout
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  0.8.4_1
gerald search for other commits by this committer
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
19 Jun 2019 08:08:31
Original commit files touched by this commit Revision:504521  0.8.4
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.2 -> 0.8.4

Reported by:	pirtscout
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  0.8.2_1
gerald search for other commits by this committer
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
26 Aug 2018 09:50:41
Original commit files touched by this commit Revision:478115  0.8.2
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.1 -> 0.8.2

Reported by:	portscout
20 Jun 2018 17:05:44
Original commit files touched by this commit Revision:472884  0.8.1_1
mat search for other commits by this committer
Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight
10 Mar 2018 17:46:06
Original commit files touched by this commit Revision:464084  0.8.1_1
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
10 Feb 2018 00:09:57
Original commit files touched by this commit Revision:461348  0.8.1
yuri search for other commits by this committer
biology/py-bx-python: Update to 0.8.1

Additional port changes:
* Changed to DISTVERSION.
* Added USE_PYTHON=cython.
* Added stripping.
* Updated maintainer e-mail.

Reported compiler warnings to the upstream.

Reported by:	portscout
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D14283
30 Nov 2017 15:50:34
Original commit files touched by this commit Revision:455210  0.7.4  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
06 May 2017 06:07:04
Original commit files touched by this commit Revision:440232  0.7.4
miwi search for other commits by this committer
bx-python is a python library and associated set of scripts to allow for rapid
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation

WWW: https://github.com/bxlab/bx-python

PR:		218757
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

Number of commits found: 16