dipcall

LOW

maintainer imjiaoyuan 0 votes scanned 2026-10-08 16:09:18.783063

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Uploaded within the last 14 days with 2 or fewer community votes — little peer review so far.

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Uploaded within the last 14 days with 2 or fewer community votes — little peer review so far.

PKGBUILD

      1# Maintainer: imjiaoyuan <imjiaoyuan@gmail.com>
    
      2# run-dipcall resolves its helpers (k8, htsbox, paftools.js, dipcall-aux.js and
    
      3# the PAR BED files) relative to its own path, so the kit is installed as a
    
      4# directory and exposed through an exec wrapper that keeps that path. k8 and
    
      5# htsbox wrappers exec the packaged binaries. paftools.js is taken from the
    
      6# minimap2 release matching the pinned version.
    
      7
    
      8pkgname=dipcall
    
      9pkgver=0.3
    
      10pkgrel=1
    
      11pkgdesc="Reference-based variant calling pipeline for diploid assemblies"
    
      12arch=('any')
    
      13url="https://github.com/lh3/dipcall"
    
      14license=('MIT')
    
      15depends=('bedtk' 'htsbox' 'k8-bin' 'minimap2' 'perl' 'samtools')
    
      16optdepends=('winnowmap: mapping with a repetitive k-mer list (-W)')
    
      17source=("dipcall-$pkgver.tar.gz::$url/archive/v$pkgver.tar.gz"
    
      18        "paftools.js::https://raw.githubusercontent.com/lh3/minimap2/v2.31/misc/paftools.js")
    
      19sha256sums=('d7f711105abc24346c03b8b082adb1427462646c5aed5dd7f48712ab6d1991c3'
    
      20            'c788e2e41b7fe6f2df05f2d4bb8dbb7b4fc5c42a1759e7666b7b2f7ffca8fd8f')
    
      21
    
      22package() {
    
      23    cd "$srcdir/dipcall-$pkgver"
    
      24    install -d "$pkgdir/usr/lib/$pkgname"
    
      25    install -m755 run-dipcall "$pkgdir/usr/lib/$pkgname/run-dipcall"
    
      26    install -m644 dipcall-aux.js "$pkgdir/usr/lib/$pkgname/dipcall-aux.js"
    
      27    install -m644 "$srcdir/paftools.js" "$pkgdir/usr/lib/$pkgname/paftools.js"
    
      28    install -m644 data/*.bed "$pkgdir/usr/lib/$pkgname/"
    
      29    for helper in k8 htsbox; do
    
      30        printf '#!/bin/sh\nexec /usr/bin/%s "$@"\n' "$helper" \
    
      31            > "$pkgdir/usr/lib/$pkgname/$helper"
    
      32        chmod 755 "$pkgdir/usr/lib/$pkgname/$helper"
    
      33    done
    
      34    install -d "$pkgdir/usr/bin"
    
      35    printf '#!/bin/sh\nexec /usr/lib/dipcall/run-dipcall "$@"\n' \
    
      36        > "$pkgdir/usr/bin/run-dipcall"
    
      37    chmod 755 "$pkgdir/usr/bin/run-dipcall"
    
      38    install -Dm644 LICENSE.txt "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
    
      39}
    
      40

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Scanned at (UTC)	Severity	Rules
2026-10-08 16:09:18	Low	1