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Port details
haplohseq Identify regions of allelic imbalance
0.1.2_6 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 Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-09-16 01:07:39
Last Update: 2023-01-16 19:32:07
Commit Hash: e1287d0
License: MIT
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (14 items)
Collapse this list.
  1. /usr/local/share/licenses/haplohseq-0.1.2_6/catalog.mk
  2. /usr/local/share/licenses/haplohseq-0.1.2_6/LICENSE
  3. /usr/local/share/licenses/haplohseq-0.1.2_6/MIT
  4. bin/haplohseq
  5. bin/haplohseq-example
  6. share/examples/haplohseq/example/example_input/tumor_exome.vcf
  7. share/examples/haplohseq/example/example_run.sh
  8. share/examples/haplohseq/ldmap/hg19.exome.ldmap
  9. share/examples/haplohseq/scripts/haplohseq_plot.R
  10. share/examples/haplohseq/scripts/ldmap.py
  11. share/examples/haplohseq/scripts/simple_phaser.py
  12. @owner
  13. @group
  14. @mode
Collapse this list.
Dependency lines:
  • haplohseq>0:biology/haplohseq
To install the port:
cd /usr/ports/biology/haplohseq/ && make install clean
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:

Packages (timestamps in pop-ups are UTC):
haplohseq
ABIlatestquarterly
FreeBSD:11:aarch64pkg-fallout0.1.2_2
FreeBSD:11:amd640.1.2_30.1.2_3
FreeBSD:11:armv6pkg-fallout0.1.2_2
FreeBSD:11:i3860.1.2_30.1.2_3
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout0.1.2_5
FreeBSD:12:amd640.1.2_60.1.2_5
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3860.1.2_60.1.2_5
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-fallout0.1.2_3
FreeBSD:13:aarch640.1.2_60.1.2_5
FreeBSD:13:amd640.1.2_60.1.2_5
FreeBSD:13:armv60.1.2_2pkg-fallout
FreeBSD:13:armv70.1.2_60.1.2_5
FreeBSD:13:i3860.1.2_60.1.2_5
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout0.1.2_5
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch640.1.2_5pkg-fallout
FreeBSD:14:amd640.1.2_6pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv70.1.2_5pkg-fallout
FreeBSD:14:i3860.1.2_6pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc640.1.2_5pkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. R-cran-optparse>0 : devel/R-cran-optparse
  2. python3.9 : lang/python39
Library dependencies:
  1. libboost_system.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/outpaddling/haplohseq/tar.gz/0.1.2?dummy=/
Collapse this list.

Number of commits found: 15

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.1.2_6
16 Jan 2023 19:32:07
commit hash:e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash:e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash:e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash:e1287d0d1228d93e469256fa6c4c824b9d20426b files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*:	bump libboost*.so libraries consumert after Boost upgrade
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)
0.1.2_5
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)
0.1.2_5
12 Aug 2022 14:46:53
commit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash:4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
*/*: bump all consumers after recent boost upgrade
0.1.2_4
22 May 2022 20:17:16
commit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash:b082b3d13e8c4872b73fb681eb99b261926ac9cd files touched by this commit
Dima Panov (fluffy) search for other commits by this committer
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
0.1.2_3
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.1.2_3
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.1.2_3
23 Jan 2021 19:31:50
Revision:562414Original commit files touched by this commit
jwb search for other commits by this committer
biology/haplohseq: Fix example scripts for python 3

Also clean up plist
0.1.2_2
15 Jan 2021 00:08:06
Revision:561615Original commit files touched by this commit
jwb search for other commits by this committer
biology/haplohseq: Restrict to python3

Also remove extraneous @dir from plist

Reported by:    rene
0.1.2_2
14 Jan 2021 15:51:19
Revision:561567Original commit files touched by this commit
jwb search for other commits by this committer
biology/haplohseq: Resurrect and fix python2 dependency

Move upstream to Github fork
0.1.2_2
19 Sep 2020 13:01:00
Revision:548980Original commit files touched by this commit
rene search for other commits by this committer
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 View all of this commit message)
0.1.2_2
08 Mar 2020 17:01:47
Revision:528058Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate some ports using deprecated version of python

With hat:	portmgr
0.1.2_2
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit
jbeich search for other commits by this committer
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
Revision:517828Original commit files touched by this commit
jwb search for other commits by this committer
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
Revision:512137Original commit files touched by this commit
jwb search for other commits by this committer
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.

Number of commits found: 15