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Port details
py-pywgsim Modified wgsim genomic data simulator
0.5.2_1 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 0.5.2Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-09-06 12:57:08
Last Update: 2024-06-07 08:11:35
Commit Hash: de4b547
Also Listed In: python
License: MIT
WWW:
https://pypi.python.org/pypi/pywgsim
Description:
pywgsim is a modified version of the wgsim short read simulator. The code for wgsim has been modified to allow visualizing the simulated mutations as a GFF file.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

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:
  • py311-pywgsim>0:biology/py-pywgsim
To install the port:
cd /usr/ports/biology/py-pywgsim/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-pywgsim
  • pkg install py311-pywgsim
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: py311-pywgsim
Package flavors (<flavor>: <package>)
  • py311: py311-pywgsim
distinfo:
TIMESTAMP = 1630888272 SHA256 (pywgsim-0.5.2.tar.gz) = b6726be21629bd1cda12592b536dcd62d250fc4872e47cbcc54066e8a6e8f709 SIZE (pywgsim-0.5.2.tar.gz) = 81724

Packages (timestamps in pop-ups are UTC):
py311-pywgsim
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.5.2_10.5.2_1-0.5.2_10.5.2_1---
FreeBSD:13:quarterly--------
FreeBSD:14:latest-0.5.2_1--0.5.2_1---
FreeBSD:14:quarterly--------
FreeBSD:15:latest0.5.2_10.5.2_1n/a-n/a---
 

py39-pywgsim
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.5.20.5.2-0.5.20.5.2---
FreeBSD:13:quarterly0.5.20.5.20.5.20.5.20.5.20.5.20.5.20.5.2
FreeBSD:14:latest0.5.20.5.20.5.20.5.20.5.20.5.2-0.5.2
FreeBSD:14:quarterly0.5.20.5.2-0.5.20.5.20.5.20.5.20.5.2
FreeBSD:15:latest--n/a0.5.2n/a0.5.20.5.20.5.2
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. cython-3.11 : lang/cython@py311
  2. py311-setuptools>=63.1.0 : devel/py-setuptools@py311
  3. python3.11 : lang/python311
Test dependencies:
  1. python3.11 : lang/python311
Runtime dependencies:
  1. py311-plac>=0 : devel/py-plac@py311
  2. py311-setuptools>=63.1.0 : devel/py-setuptools@py311
  3. python3.11 : lang/python311
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_py-pywgsim
USES:
python
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/p/pywgsim/
  2. https://pypi.org/packages/source/p/pywgsim/
Collapse this list.

Number of commits found: 8

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.5.2_1
07 Jun 2024 08:11:35
commit hash: de4b547a33bff2efe0ccd8f8a50b3919ae19d4fbcommit hash: de4b547a33bff2efe0ccd8f8a50b3919ae19d4fbcommit hash: de4b547a33bff2efe0ccd8f8a50b3919ae19d4fbcommit hash: de4b547a33bff2efe0ccd8f8a50b3919ae19d4fb files touched by this commit
Ruslan Makhmatkhanov (rm) search for other commits by this committer
biology/py-pywgsim: fix build

cython dependency not available at post-patch stage. Use post-configure instead

Approved by:	portmgr (blanket approval)
0.5.2_1
04 Jun 2024 11:55:31
commit hash: 91e7916b1c0954e949a0482cfda80ad5ff57767bcommit hash: 91e7916b1c0954e949a0482cfda80ad5ff57767bcommit hash: 91e7916b1c0954e949a0482cfda80ad5ff57767bcommit hash: 91e7916b1c0954e949a0482cfda80ad5ff57767b files touched by this commit
Ruslan Makhmatkhanov (rm) search for other commits by this committer
biology/py-pywgsim: unbreak with python3.11

make it recreate the source with newer cython

PR:		275494
Approved by:	portmgr (blanket approval)
0.5.2_1
03 Jun 2024 12:18:08
commit hash: f1e51f12a7764df202789983ccb49abb47dbfde8commit hash: f1e51f12a7764df202789983ccb49abb47dbfde8commit hash: f1e51f12a7764df202789983ccb49abb47dbfde8commit hash: f1e51f12a7764df202789983ccb49abb47dbfde8 files touched by this commit
Antoine Brodin (antoine) search for other commits by this committer
biology/py-pywgsim: unbreak bulk -a
0.5.2_1
03 Jun 2024 11:41:44
commit hash: 155267db532b5a457166b625b9e7f0a0bf0280a3commit hash: 155267db532b5a457166b625b9e7f0a0bf0280a3commit hash: 155267db532b5a457166b625b9e7f0a0bf0280a3commit hash: 155267db532b5a457166b625b9e7f0a0bf0280a3 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/py-pywgsim: Limit to python 3.10

Nontrivial changes needed for python 3.11
Abandoned upstream

Reported by:    pkg-fallout
0.5.2
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
0.5.2
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
0.5.2
06 Sep 2021 12:55:49
commit hash: c085af1e81472458f64d957aab5e9a9e0580d8cacommit hash: c085af1e81472458f64d957aab5e9a9e0580d8cacommit hash: c085af1e81472458f64d957aab5e9a9e0580d8cacommit hash: c085af1e81472458f64d957aab5e9a9e0580d8ca files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/py-pywgsim: Modified wgsim genomic data simulator

pywgsim is a modified version of the wgsim short read simulator.  The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.

Number of commits found: 8