| Port details |
- py-gffutils Work with GFF and GTF files in a flexible database framework
- 0.13_1 biology
 =2      0.13Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-10-19 02:07:07
- Last Update: 2025-03-08 04:05:21
- Commit Hash: 06a08e6
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py311-PyOpenGL, p5-Sane
- Also Listed In: python
- License: MIT
- WWW:
- https://github.com/daler/gffutils
- Description:
- gffutils is a Python package for working with and manipulating the GFF and GTF
format files typically used for genomic annotations. Files are loaded into a
sqlite3 database, allowing much more complex manipulation of hierarchical
features (e.g., genes, transcripts, and exons) than is possible with plain-text
methods alone.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}gffutils>0:biology/py-gffutils@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-gffutils/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-gffutils
- pkg install py311-gffutils
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py311-gffutils listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-gffutils
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1718571181
SHA256 (gffutils-0.13.tar.gz) = b0d52f35c014cc0330fb5c4e3c6fea127c90ccf4c5384a825cdb5c8ff330d4eb
SIZE (gffutils-0.13.tar.gz) = 1560489
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:
-
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- Test dependencies:
-
- py311-pytest>=7,1 : devel/py-pytest@py311
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-argcomplete>=1.9.4 : devel/py-argcomplete@py311
- py311-argh>=0.26.2 : devel/py-argh@py311
- py311-pyfaidx>=0.5.5.2 : biology/py-pyfaidx@py311
- py311-simplejson>0 : devel/py-simplejson@py311
- py311-six>=1.12.0 : devel/py-six@py311
- python3.11 : lang/python311
- There are no ports dependent upon this port
Configuration Options:- No options to configure
- Options name:
- biology_py-gffutils
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.13_1
08 Mar 2025 04:05:21
 |
Charlie Li (vishwin) |
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
Any missed ports, feel free to bump.
Any ports that need setuptools at runtime can have the devel/py-setuptools
manually added back to RUN_DEPENDS, but understand that this practice
is deprecated; see CHANGES for details. |
0.13
17 Jun 2024 01:20:35
|
Yuri Victorovich (yuri) |
biology/py-gffutils: update 0.11.1 → 0.13 |
0.11.1
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
all: remove explicit versions in USES=python for "3.x+"
The logic in USES=python will automatically convert this to 3.8+ by
itself.
Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.
finance/quickfix: mark BROKEN with PYTHON
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
^~~~~~~~~~
1 warning and 1 error generated.
Reviewed by: portmgr, vishwin, yuri
Differential Revision: <https://reviews.freebsd.org/D40568> |
0.11.1
12 Mar 2023 09:02:31
|
Yuri Victorovich (yuri) |
biology/py-gffutils: Update 0.11.0 → 0.11.1
Reported by: portscout |
0.11.0
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
Remove WWW entries moved into port Makefiles
Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.
This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.
Approved by: portmgr (tcberner) |
0.11.0
07 Sep 2022 21:10:59
|
Stefan Eßer (se) |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above  ) |
0.11.0
07 Jun 2022 00:38:48
|
Yuri Victorovich (yuri) |
biology/py-gffutils: Update 0.10.1 -> 0.11.0
Reported by: portscout |
0.10.1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.10.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.10.1
14 Jul 2020 07:59:28
 |
antoine |
Unbreak bulk -a |
0.10.1
16 Jun 2020 02:10:08
|
yuri |
biology/py-gffutils: Update 0.10 -> 0.10.1 |
0.10
31 Dec 2019 05:16:09
|
yuri |
biology/py-gffutils: Update 0.9 -> 0.10
Reported by: portscout |
0.9_1
10 Apr 2019 06:18:32
|
antoine |
Bump a few PORTREVISIONs after r498529
With hat: portmgr |
0.9
19 Oct 2018 02:06:54
|
yuri |
New port: biology/py-gffutils: Work with GFF and GTF files in a flexible
database framework |
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