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Port details
haplohseq Identify regions of allelic imbalance
0.1.2_2 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 0.1.2Version 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: 2019-12-11 17:53:49
SVN Revision: 519824
License: MIT
Description:
SVNWeb : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (14 items)
  1. /usr/local/share/licenses/haplohseq-0.1.2_2/catalog.mk
  2. /usr/local/share/licenses/haplohseq-0.1.2_2/LICENSE
  3. /usr/local/share/licenses/haplohseq-0.1.2_2/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/ldmap.py.orig
  12. share/examples/haplohseq/scripts/simple_phaser.py
  13. share/examples/haplohseq/scripts/simple_phaser.py.orig
  14. @dir share/examples/haplohseq/example/example_output
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: pkg install haplohseq
PKGNAME: haplohseq
Flavors: there is no flavor information for this port.
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake : devel/gmake
  2. python2.7 : lang/python27
Runtime dependencies:
  1. R-cran-optparse>0 : devel/R-cran-optparse
  2. python2.7 : lang/python27
Library dependencies:
  1. libboost_system.so : devel/boost-libs
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://acadix.biz/Ports/distfiles/

Number of commits found: 3

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Dec 2019 17:53:49
Original commit files touched by this commit  0.1.2_2
Revision:519824
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
17 Nov 2019 15:00:13
Original commit files touched by this commit  0.1.2_1
Revision:517828
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
16 Sep 2019 01:07:31
Original commit files touched by this commit  0.1.2
Revision:512137
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: 3

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