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Port details
bcf-score Bcftools plugins for GWAS-VCF summary statistics files
1.16_1 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 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: 2023-07-16 13:19:06
Commit Hash: 63e5ba4
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 (12 items)
Collapse this list.
  1. /usr/local/share/licenses/bcf-score-1.16_1/catalog.mk
  2. /usr/local/share/licenses/bcf-score-1.16_1/LICENSE
  3. /usr/local/share/licenses/bcf-score-1.16_1/MIT
  4. libexec/bcftools/blupx.so
  5. libexec/bcftools/liftover.so
  6. libexec/bcftools/metal.so
  7. libexec/bcftools/munge.so
  8. libexec/bcftools/score.so
  9. share/bcf-score/assoc_plot.R
  10. @owner
  11. @group
  12. @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 = 1677335027 SHA256 (score_1.16-20221221.tar.gz) = f5f7331f2f670ea26cbc48a924e1467ac13c69aaf3b2a56599e3decda9375c0b SIZE (score_1.16-20221221.tar.gz) = 61927

Expand this list (2 items)

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SHA256 (samtools-bcftools-1.16-1.17_GH0.tar.gz) = e6fdb4c94b531671ea8a0b00cb9245aa2602f6c4480621e45dac76338f590b9e SIZE (samtools-bcftools-1.16-1.17_GH0.tar.gz) = 3481344

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Packages (timestamps in pop-ups are UTC):
bcf-score
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.16_11.16_1-1.16_11.16_1---
FreeBSD:13:quarterly1.16_11.16_11.161.16_11.16_11.16_11.16_11.16_1
FreeBSD:14:latest1.16_11.16_1-1.16_11.16_11.16-1.16
FreeBSD:14:quarterly1.16_11.16_1-1.16_11.16_11.16_11.16_11.16_1
FreeBSD:15:latest1.16_11.16_1n/a1.16_1n/a1.16_11.16_11.16_1
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. bash : shells/bash
  2. gmake>=4.3 : devel/gmake
  3. autoconf>=2.71 : devel/autoconf
  4. automake>=1.16.5 : devel/automake
Test dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. bcftools>=1.16 : biology/bcftools
Library dependencies:
  1. libhts.so : biology/htslib
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/1.17?dummy=/
  2. https://software.broadinstitute.org/software/score/
Collapse this list.

Number of commits found: 2

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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: 2