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Port details on branch 2022Q2
haplohseq Identify regions of allelic imbalance
0.1.2_11 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 0.1.2_11Version 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: 2024-02-13 14:44:22
Commit Hash: db61653
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
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_11/catalog.mk
  2. /usr/local/share/licenses/haplohseq-0.1.2_11/LICENSE
  3. /usr/local/share/licenses/haplohseq-0.1.2_11/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:
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):
haplohseq
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.1.2_110.1.2_110.1.2_20.1.2_110.1.2_11---
FreeBSD:13:quarterly0.1.2_110.1.2_11-0.1.2_110.1.2_11-0.1.2_100.1.2_10
FreeBSD:14:latest0.1.2_110.1.2_11-0.1.2_110.1.2_11---
FreeBSD:14:quarterly0.1.2_100.1.2_11-0.1.2_100.1.2_11-0.1.2_100.1.2_10
FreeBSD:15:latest0.1.2_110.1.2_11n/a0.1.2_10n/a-0.1.2_100.1.2_11
FreeBSD:15:quarterly--n/a-n/a---
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:
===> The following configuration options are available for haplohseq-0.1.2_11: 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/outpaddling/haplohseq/tar.gz/0.1.2?dummy=/
Collapse this list.

There are no commits on branch 2022Q2 for this port
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