| Port details |
- py-pyfaidx Efficient pythonic random access to fasta subsequences
- 0.5.9.5 biology
 =2      0.5.9.5Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-10-19 02:05:49
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: BSD3CLAUSE
- WWW:
- https://github.com/mdshw5/pyfaidx
- Description:
- FASTA is a format to exchange generic information, partial or of the entire
organism.
A function "faidx" (FAsta InDeX) creates a small flat index file ".fai" allowing
for fast random access to any subsequence in the indexed FASTA file, while
loading a minimal amount of the file in to memory. This python module implements
pure Python classes for indexing, retrieval, and in-place modification of FASTA
files using a samtools compatible index. The pyfaidx module is API compatible
with the pygr seqdb module. A command-line script "faidx" is installed alongside
the pyfaidx module, and facilitates complex manipulation of FASTA files without
any programming knowledge.
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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:
-
- ${PYTHON_PKGNAMEPREFIX}pyfaidx>0:biology/py-pyfaidx@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-pyfaidx/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-pyfaidx
- pkg install py39-pyfaidx
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 py39-pyfaidx listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-pyfaidx
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1619213645
SHA256 (pyfaidx-0.5.9.5.tar.gz) = 9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b
SIZE (pyfaidx-0.5.9.5.tar.gz) = 32772
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:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-six>0 : devel/py-six@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/py-gffutils
Configuration Options:- No options to configure
- Options name:
- biology_py-pyfaidx
- 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 |
|---|
0.5.9.5
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> |
0.5.9.5
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) |
0.5.9.5
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  ) |
0.5.9.5
23 Apr 2021 21:57:50
|
Yuri Victorovich (yuri) |
biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5 |
0.5.9.2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.5.9.2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.5.9.2
28 Dec 2020 23:02:15
 |
antoine |
Drop python 2.7 support from a few ports
With hat: portmgr |
0.5.9.2
17 Dec 2020 02:40:59
|
yuri |
biology/py-pyfaidx: Update 0.5.9.1 -> 0.5.9.2
Reported by: portscout |
0.5.9.1
13 Sep 2020 19:05:30
|
yuri |
biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1 |
0.5.5.2_1
10 Apr 2019 06:18:32
|
antoine |
Bump a few PORTREVISIONs after r498529
With hat: portmgr |
0.5.5.2
28 Oct 2018 04:34:15
|
yuri |
biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2
Reported by: portscout |
0.5.5.1
19 Oct 2018 02:05:37
|
yuri |
New port: biology/py-pyfaidx: Efficient pythonic random access to fasta
subsequences |
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