Add PLINK 1.9

[adityaruplaha]

Involved packages

• PLINK 1.9 from https://www.cog-genomics.org/plink/1.9/, https://aur.archlinux.org/packages/plink1.9-git

As previously discussed.

Details

• Tested in the local machine (largest 16G RAM) and it is passed without any issue
• Provide New Package
• Fix the Packages
  • PKGBUILD
  • lilac.yaml
  • lilac.py
• Would like to continue to work with us

[Copilot]

Pull request overview

This pull request adds PLINK 1.9, a whole-genome association analysis toolset, to BioArchLinux. The package is configured to track releases from the chrchang/plink-ng GitHub repository and builds from source with custom patches.

Key Changes:

• New package configuration for plink1.9 with git-based versioning tracking the plink-ng repository
• PKGBUILD defining build process including preparation, build, and installation steps with custom patching
• Lilac configuration for automated updates from GitHub releases

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
BioArchLinux/plink1.9/lilac.yaml	Configures automated package management with GitHub source tracking for version 1.9 releases and post-build git commit automation
BioArchLinux/plink1.9/PKGBUILD	Defines package build process including source retrieval, patching, compilation flags, and installation for plink1.9-git package

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[kbipinkumar]

use_latest_release option will retrieve latest release tag v2.0.0-a.6.29
from git repo. however the sources array in the PKGBUILD is using git as source without any tag attached.

[adityaruplaha]

I may have misunderstood how lilac works. The following is my understanding of what's going on:

• The PKGBUILD always pulls in the latest commit.
• The update_on section is triggered everytime there's a new release. I couldn't find a way to restrict this to just v1.9 releases, so this is essentially a compromise.

If more stability is desirable, I can checkout the last available v1.9 tag in prepare(). If more frequent updates are desirable, then I can drop this line so that we have updates on every commit (like on AUR).

[kbipinkumar]

not claiming to be an expert on lilac per se. i believe you can specify specific tag in git sources in PKGBUILD like this

pkgver=1.9.0-b.7.10
_tag=v${pkgver}
source=('plink1.9::git+https://github.com/chrchang/plink-ng.git#tag=$_tag')

and then fix this specific version/tag in lilac.yaml like this

update_on:
  - source: github
    github: chrchang/plink-ng
    use_latest_release: true
    prefix: 'v'
 
update_on:
  - source: manual
    manual: 1.9.0-b.7.10

this should in theory keep the package at the latest 1.9 version. the downside is you will have to manually increment version number in the yaml to trigger an update.

@lilydjwg or @sukanka can confirm whether what i said here is correct or not.

[lilydjwg]

If you want 1.9.x, you can use use_max_tag with include_regex.

[adityaruplaha]

@kbipinkumar

i believe you can specify specific tag in git sources in PKGBUILD like this

I know, but that pins me to a specific version, not the latest tagged 1.9.

the downside is you will have to manually increment version number in the yaml to trigger an update.

Precisely what I want to avoid.

[adityaruplaha]

@lilydjwg Thanks, I'll give that a shot.

[starsareintherose]

I will invite you as co maintainer once this pr is merged, though I am on leave

[sukanka]

I think it is not version 1.9.x, though it is named plink-1.9. The latest version is v2.0.0-a.6.29, and the PKGBUILD uses plain vcs source with no commit or tag pinned, so it will keep up with the latest commit (version 2.0.0 and later)

[adityaruplaha]

@sukanka No, that's a quirk of the repo structure. Both 1.9 and 2.0 live under the same source tree; that's why we use --match in pkgver() to get the right tag.

This is how it's handled on AUR; please correct me if its not the same here.

[sukanka]

@sukanka No, that's a quirk of the repo structure. Both 1.9 and 2.0 live under the same source tree; that's why we use --match in pkgver() to get the right tag.

This is how it's handled on AUR; please correct me if its not the same here.

Oh. I see, there are 1.9 and 2.0 under the same directory.