notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)Want a good monitor light? See my photosAll times are UTC		 Ukraine
2024-11-06 Today brought in a new category: filesystems. Sadly, the website did not process it well. I am working on that. It may take a few days.
2024-11-07 Commit processing is halted. I have a fix for the new category. It is making its way through the system.
UPDATE: the backend is processing the original filesystems commit now. It should take about an hour.
UPDATE: as of 20:30 UTC, the filesystems commit has been processed. Commit processing is now up to date.
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)

Collapse this list.

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

Collapse this list.

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
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
Security Policy
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
chromiumNov 16
electron31*Nov 16
electron32*Nov 16
ungoogled-chromiumNov 16
vaultwardenNov 16
electron31Nov 14
gitlabNov 14
postgresql12-clientNov 14
postgresql12-plperlNov 14
postgresql12-serverNov 14
postgresql12-serverNov 14
postgresql13-clientNov 14
postgresql13-plperlNov 14
postgresql13-serverNov 14
postgresql13-serverNov 14

20 vulnerabilities affecting 151 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last processed:
2024-11-16 12:24:49 UTC


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)

Calculated hourly:
Port count 32997
Broken 104
Deprecated 174
Ignore 233
Forbidden 1
Restricted 2
No CDROM 1
Vulnerable 47
Expired 12
Set to expire 136
Interactive 0
new 24 hours 0
new 48 hours12
new 7 days29
new fortnight220
new month289
Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD 		Valid HTML, CSS, and RSS. Copyright © 2000-2024 Dan Langille. All rights reserved.