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Port details
bcf-score Bcftools plugins for GWAS-VCF summary statistics files
1.20 biology on this many watch lists=2 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 1.16_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2023-02-25 14:30:08
Last Update: 2024-10-09 22:23:09
Commit Hash: 384625e
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
License: MIT
WWW:
https://software.broadinstitute.org/software/score/
Description:
Score is a set of tools in the form of a bcftools plugin, for handling and converting summary statistics files following the GWAS-VCF specification.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (13 items)
Collapse this list.
  1. /usr/local/share/licenses/bcf-score-1.20/catalog.mk
  2. /usr/local/share/licenses/bcf-score-1.20/LICENSE
  3. /usr/local/share/licenses/bcf-score-1.20/MIT
  4. libexec/bcftools/blup.so
  5. libexec/bcftools/liftover.so
  6. libexec/bcftools/metal.so
  7. libexec/bcftools/munge.so
  8. libexec/bcftools/pgs.so
  9. libexec/bcftools/score.so
  10. share/bcf-score/assoc_plot.R
  11. @owner
  12. @group
  13. @mode
Collapse this list.
Dependency lines:
  • bcf-score>0:biology/bcf-score
To install the port:
cd /usr/ports/biology/bcf-score/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bcf-score
  • pkg install bcf-score
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bcf-score
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1727475307 SHA256 (score_1.20-20240505.tar.gz) = c2ac510f0a48e3d2e61d1a9e219e030b1268cdcf3bf987217bbd16740d962d41 SIZE (score_1.20-20240505.tar.gz) = 96852

Expand this list (2 items)

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SHA256 (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 7484695c5d833fb1a89c2b886ec302db0514ba3c8e5ef7397b9302fa8bd37f8d SIZE (samtools-bcftools-1.20-1.21_GH0.tar.gz) = 3665160

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Packages (timestamps in pop-ups are UTC):
bcf-score
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.201.20--1.20---
FreeBSD:13:quarterly1.16_11.16_11.161.16_11.16_11.16_11.16_11.16_1
FreeBSD:14:latest1.201.20--1.201.16-1.16
FreeBSD:14:quarterly1.16_11.16_1-1.16_11.16_11.16_11.16_11.16_1
FreeBSD:15:latest1.201.20n/a-n/a1.16_11.16_11.16_1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. htslib>=1.21 : biology/htslib
  2. gmake>=4.4.1 : devel/gmake
  3. autoconf>=2.72 : devel/autoconf
  4. automake>=1.17 : devel/automake
Test dependencies:
  1. bash : shells/bash
  2. perl5>=5.36<5.37 : lang/perl5.36
Runtime dependencies:
  1. bash : shells/bash
  2. bcftools>=1.20 : biology/bcftools
Library dependencies:
  1. libhts.so : biology/htslib
  2. libcholmod.so : math/suitesparse-cholmod
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_bcf-score
USES:
autoreconf gmake localbase perl5 python:env shebangfix
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://codeload.github.com/samtools/bcftools/tar.gz/1.21?dummy=/
  2. https://software.broadinstitute.org/software/score/
Collapse this list.

Number of commits found: 3

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.20
09 Oct 2024 22:23:09
commit hash: 384625e2db650bbc95ae66326590e67357126009commit hash: 384625e2db650bbc95ae66326590e67357126009commit hash: 384625e2db650bbc95ae66326590e67357126009commit hash: 384625e2db650bbc95ae66326590e67357126009 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bcf-score: Update to 1.20

Numerous bug fixes and enhancements since 1.16

Reported by:    portscout
1.16_1
16 Jul 2023 13:19:06
commit hash: 63e5ba4396f40d97df99b2856113afcb7623d7c9commit hash: 63e5ba4396f40d97df99b2856113afcb7623d7c9commit hash: 63e5ba4396f40d97df99b2856113afcb7623d7c9commit hash: 63e5ba4396f40d97df99b2856113afcb7623d7c9 files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bcf-score: Unbreak build with clang 16

Patch function pointer assignments that went from warning to error
with the compiler upgrade

Reported by:    pkg-fallout
1.16
25 Feb 2023 14:27:46
commit hash: 68c12d4ad402d885c078499f05c4a3919276398bcommit hash: 68c12d4ad402d885c078499f05c4a3919276398bcommit hash: 68c12d4ad402d885c078499f05c4a3919276398bcommit hash: 68c12d4ad402d885c078499f05c4a3919276398b files touched by this commit		 Jason W. Bacon (jwb) search for other commits by this committer 
biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics

Score is a set of tools in the form of a bcftools plugin, for handling
and converting summary statistics files following the GWAS-VCF
specification.

Number of commits found: 3
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