| Port details |
- peak-classifier Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
- 0.1.4.13_1 biology
 =2      0.1.4.13_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-06-14 16:45:08
- Last Update: 2024-04-05 00:43:40
- Commit Hash: ce6eaa8
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSD2CLAUSE
- WWW:
- https://github.com/auerlab/peak-classifier
- Description:
- Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
Peaks are provided in a BED file sorted by chromosome and position. The GFF
must be sorted by chromosome and position, with gene-level features separated
by ### tags and each gene organized into subfeatures such as transcripts and
exons. This is the default for common data sources.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- peak-classifier>0:biology/peak-classifier
- To install the port:
- cd /usr/ports/biology/peak-classifier/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/peak-classifier
- pkg install peak-classifier
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: peak-classifier
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1694019604
SHA256 (auerlab-peak-classifier-0.1.4-13-gfb89af3_GH0.tar.gz) = 83fd1032eb3ab8b92ffbbf9f06da1b18cf93a39bc01aba249961550e548c0df1
SIZE (auerlab-peak-classifier-0.1.4-13-gfb89af3_GH0.tar.gz) = 87429
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:
-
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- bedtools : biology/bedtools
- py39-matplotlib>0 : math/py-matplotlib@py39
- python3.9 : lang/python39
- Library dependencies:
-
- libxtend.so : devel/libxtend
- libbiolibc.so : biology/biolibc
- This port is required by:
- for Run
-
- biology/atac-seq
- biology/chip-seq
Configuration Options:- No options to configure
- Options name:
- biology_peak-classifier
- USES:
- localbase 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 |
|---|
0.1.4.13_1
05 Apr 2024 00:43:40
 |
Po-Chuan Hsieh (sunpoet) |
biology/peak-classifier: Clean up USES=python
- Fix d6b521a455883ea2b387fb9cf61637ea879b746c
- Reapply 1d86601d3200c531e7fcd174cdd1feaf6d616518
USES=python means USES=python:3.8+ now.
Approved by: portmgr (blanket)
With hat: python |
0.1.4.13_1
02 Mar 2024 19:37:42
|
Nuno Teixeira (eduardo) |
biology/peak-classifier: Move man pages to share/man
Approved by: portmgr (blanket) |
0.1.4.13
28 Oct 2023 11:38:43
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.4.13
Updates for new libxtend API |
0.1.4.11
06 Sep 2023 20:50:36
|
Po-Chuan Hsieh (sunpoet) |
biology/peak-classifier: Clean up USES=python
Approved by: portmgr (blanket)
With hat: python |
0.1.4.11
11 Aug 2023 20:44:14
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.4.11
Updates for biolibc GFF3 API changes |
0.1.4.8
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> |
0.1.4.8
10 Jun 2023 11:57:56
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.4.8
Updates for libxtend API
Minor fixes |
0.1.4.5_1
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
0.1.4.5
11 Dec 2022 20:09:20
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.4-5
Update for biolibc API changes |
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) |
0.1.4
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  ) |
0.1.4
11 Jun 2022 14:26:57
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.4
Update for bl_gff_t API streamlining
Changes: https://github.com/auerlab/peak-classifier/tags |
0.1.3
15 Mar 2022 21:41:51
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.3
Minor update for biolibc 0.2.2 API changes |
0.1.2
14 Dec 2021 19:45:32
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.2
Mainly updates for evolving libxtend and biolibc APIs
A few minor fixes and enhancements |
0.1.1.21
02 Sep 2021 23:15:40
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.1.21
Fix regression: Replace BL_BED_SET_STRAND() macro with
bl_bed_set_strand(), which performs sanity checks |
0.1.1.20
28 Aug 2021 01:34:46
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Update to 0.1.1.20
Updates for libxtend and biolibc API changes |
0.1.1
14 Jun 2021 16:40:33
|
Jason W. Bacon (jwb) |
biology/peak-classifier: Classify peaks based on GFF features
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons. This is the default for
common data sources. |
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