| Port details |
- py-macs2 Identify transcription factor binding sites
- 2.2.9.1 biology
 =2      2.2.9.1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2017-12-02 20:46:35
- Last Update: 2023-08-06 18:17:52
- Commit Hash: e97c345
- 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/taoliu/MACS
- Description:
- MACS is a tool for chromatin immunoprecipitation (ChIP) sequence analysis.
MACS empirically models the length of the sequenced ChIP fragments, which
tend to be shorter than sonication or library construction size estimates,
and uses it to improve the spatial resolution of predicted binding sites.
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}macs2>0:biology/py-macs2@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-macs2/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-macs2
- pkg install py39-macs2
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-macs2 listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-macs2
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1691269587
SHA256 (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 8e461dde82288280fe708cd4f5fec986fbf2da67b344f4dea5693af849549163
SIZE (taoliu-MACS-v2.2.9.1_GH0.tar.gz) = 133109075
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-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
- cython-3.9 : lang/cython@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- py39-pytest>0 : devel/py-pytest@py39
- bash : shells/bash
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
- py39-cykhash>0 : devel/py-cykhash@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/atac-seq
- biology/chip-seq
Configuration Options:- No options to configure
- Options name:
- biology_py-macs2
- USES:
- python shebangfix
- 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 |
|---|
2.2.9.1
06 Aug 2023 18:17:52
 |
Jason W. Bacon (jwb) |
biology/py-macs2: Update to 2.2.9.1
Mainly updates to dependencies
Changes: https://github.com/macs3-project/MACS/releases
Added test target
Reported by: portscout |
2.2.8
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> |
2.2.8
22 May 2023 17:14:04
|
Jason W. Bacon (jwb) |
biology/py-macs2: Update to 2.2.8
Adds support for python 3.11
Reported by: portscout |
2.2.7.1_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
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) |
2.2.7.1
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  ) |
2.2.7.1
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
2.2.7.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
2.2.7.1
14 Apr 2020 12:13:55
 |
jwb |
biology/py-macs2: Upgrade to 2.2.7.1
Bug fix release
Reported by: portscout |
2.2.6_1
09 Feb 2020 14:23:43
|
jwb |
biology/py-macs2: Bump revision for previous run dep addition |
2.2.6
09 Feb 2020 14:21:29
|
jwb |
biology/py-macs2: Add missing numpy run depend |
2.2.6
11 Jan 2020 14:20:00
|
jwb |
biology/py-macs2: Upgrade to 2.2.6
Bug fixes and performance improvements
Now require python 3.6+
Reported by: portscout |
2.1.0.p20170505_3
26 Jul 2019 20:46:57
|
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 |
2.1.0.p20170505_2
12 Dec 2018 01:35:36
|
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 |
2.1.0.p20170505_1
10 Mar 2018 17:46:06
|
gerald |
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079). |
2.1.0.p20170505
05 Dec 2017 02:59:01
|
jwb |
biology/py-macs2: Restrict to python 2.7.
Use ${PYNUMPY} per mat suggestion.
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D13350 |
2.1.0.p20170505
02 Dec 2017 20:46:28
 |
jwb |
[new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)
sequences
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13322 |
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