| Port details |
- haplohseq Identify regions of allelic imbalance
- 0.1.2_13 biology
 =2      0.1.2_13Version of this port present on the latest quarterly branch.  BROKEN: fails to build with Boost>=1.87
 IGNORE: is marked as broken: fails to build with Boost>=1.87
- Maintainer: jwb@FreeBSD.org
- Port Added: 2019-09-16 01:07:39
- Last Update: 2025-02-14 03:17:11
- Commit Hash: d4a2202
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: MIT
- WWW:
- https://sites.google.com/site/integrativecancergenomics/software/haplohseq
- Description:
- Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample. Input to the software includes a VCF file
of genotypes and estimated phased genotypes.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- haplohseq>0:biology/haplohseq
- To install the port:
- cd /usr/ports/biology/haplohseq/ && make install clean
- We doubt a package is available for this port because we see it marked as as:
-
Packages are normally not provided for ports that are marked as above.
- To add the package, run one of these commands:
- pkg install biology/haplohseq
- pkg install haplohseq
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: haplohseq
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1611421648
SHA256 (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 64f61023a6795decb680c23d142b1a349988d4c0e3bef8c7d52ca33bf42f29f0
SIZE (outpaddling-haplohseq-0.1.2_GH0.tar.gz) = 12084603
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:
-
- gmake>=4.4.1 : devel/gmake
- python3.11 : lang/python311
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- R-cran-optparse>0 : devel/R-cran-optparse
- python3.11 : lang/python311
- Library dependencies:
-
- libboost_system.so : devel/boost-libs
- This port is required by:
- for Run
-
- biology/mca-calling
Configuration Options:- ===> The following configuration options are available for haplohseq-0.1.2_13:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
- Options name:
- biology_haplohseq
- USES:
- compiler:c++14-lang gmake localbase:ldflags 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 |
|---|
0.1.2_13
14 Feb 2025 03:17:11
 |
Dima Panov (fluffy) |
biology/haplohseq: mark as BROKEN with Boost>=1.87 (+)
Since 1.87 release some long-time-ago deprecated Boost.asio facilities was
dropped off
Sponsored by: Future Crew, LLC |
0.1.2_13
20 Nov 2024 10:05:25
|
Dima Panov (fluffy) |
devel/boost: bump consu,ers after update Boost to 1.86 release
Sponsored by: Future Crew, LLC |
0.1.2_12
03 Oct 2024 10:25:14
|
Dima Panov (fluffy) |
*/*: bump consumers after devel/boost* update
With hat: office
Sponsored by: Future Crew, LLC |
0.1.2_11
13 Feb 2024 14:44:22
|
Dima Panov (fluffy) |
devel/boost: bump consumers after library update |
0.1.2_10
27 Sep 2023 14:36:30
|
Dima Panov (fluffy) |
devel/boost*: bump all consumers after 1.83.0 |
0.1.2_9
09 Jul 2023 16:37:39
|
Jason W. Bacon (jwb) |
biology/haplohseq: Fix build on FreeBSD 14
Add -std=c++14 to override clang 16 default
Reported by: pkg-fallout |
0.1.2_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> |
0.1.2_8
27 Apr 2023 18:25:55
|
Dima Panov (fluffy) |
*/*: bump all direct Boost cunsumers |
0.1.2_7
23 Apr 2023 09:09:58
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
0.1.2_6
16 Jan 2023 19:32:07
|
Dima Panov (fluffy) |
*/*: bump libboost*.so libraries consumert after Boost upgrade |
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) |
0.1.2_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  ) |
0.1.2_5
12 Aug 2022 14:46:53
|
Dima Panov (fluffy) |
*/*: bump all consumers after recent boost upgrade |
0.1.2_4
22 May 2022 20:17:16
|
Dima Panov (fluffy) |
devel/boost-all: bump all library consumers after boost upgrade
PR: 246106 |
0.1.2_3
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.1.2_3
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.1.2_3
23 Jan 2021 19:31:50
 |
jwb |
biology/haplohseq: Fix example scripts for python 3
Also clean up plist |
0.1.2_2
15 Jan 2021 00:08:06
|
jwb |
biology/haplohseq: Restrict to python3
Also remove extraneous @dir from plist
Reported by: rene |
0.1.2_2
14 Jan 2021 15:51:19
|
jwb |
biology/haplohseq: Resurrect and fix python2 dependency
Move upstream to Github fork |
0.1.2_2
19 Sep 2020 13:01:00
|
rene |
Remove expired ports:
2020-09-15 audio/abraca: Uses deprecated version of python
2020-09-15 audio/ardour5: Uses deprecated version of python
2020-09-15 audio/cplay: Uses deprecated version of python
2020-09-15 audio/cpp-xmms2: Uses deprecated version of python
2020-09-15 audio/p5-xmms2: Uses deprecated version of python
2020-09-15 biology/haplohseq: Uses deprecated version of python
2020-09-15 biology/tophat: Uses deprecated version of python
2020-09-15 chinese/ibus-array: Uses deprecated version of python
2020-09-15 comms/congruity: Uses deprecated version of python
2020-09-15 comms/libbtbb: Uses deprecated version of python
2020-09-15 comms/quisk: Uses deprecated version of python
2020-09-15 databases/mtools-mongodb: Uses deprecated version of python
2020-09-15 databases/mydbf2mysql: Uses deprecated version of python (Only the first 15 lines of the commit message are shown above ) |
0.1.2_2
08 Mar 2020 17:01:47
|
antoine |
Deprecate some ports using deprecated version of python
With hat: portmgr |
0.1.2_2
11 Dec 2019 17:53:49
|
jbeich |
devel/boost-*: update to 1.72.0
Changes: http://www.boost.org/users/history/version_1_72_0.html
PR: 241449
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D22136 |
0.1.2_1
17 Nov 2019 15:00:13
|
jwb |
biology/haplohseq: Switch to distfile with example data
Add script to run on example input
Minor fix to report inadequate VCF input |
0.1.2
16 Sep 2019 01:07:31
|
jwb |
biology/haplohseq: Identify regions of allelic imbalance
Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample. Input to the software includes a VCF file
of genotypes and estimated phased genotypes. |
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