bcl2fastq-bin

maintainer balwierz · 0 votes · scanned 2026-08-03 00:08:14.047287

LOW

Why flagged The package downloads a source file from the Internet Archive, but it is a verifiable, byte-identical copy of the official Illumina software, with checksums provided and no execution of remote code.

Triggered rules

LOW AI review downgraded a static finding llm_review

The static rules flagged this MEDIUM, but an AI model (qwen/qwen3-235b-a22b-07-25) reviewed the full PKGBUILD and judged it LOW (confidence 95%): The package downloads a source file from the Internet Archive, but it is a verifiable, byte-identical copy of the official Illumina software, with checksums provided and no execution of remote code.

1 higher static finding superseded - not the current verdict (shown for transparency)

MEDIUM source=() URL on a non-standard host source_untrusted_domain

One or more source=() URLs point to a host outside the trusted allowlist (github.com, gitlab.com, codeberg.org, pypi.org, …).

PKGBUILD:24 https://archive.org/download/bcl2fastq2-v"${_pkg_ver//./-}"-linux-x86-64/bcl2fastq2-v"${_pkg_ver//./-}"-linux-x86-64.zip
PKGBUILD:25 https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v"${_eula_ver}"-eula.pdf

PKGBUILD

2 offending line(s) highlighted

      1# Maintainer: Piotr Balwierz <his surname at google's email service>
    
      2# Contributor: Clint Valentine <valentine.clint@gmail.com>
    
      3
    
      4_pkg_ver=2.20.0
    
      5_pkg_build=422
    
      6_eula_ver=2-20
    
      7_guide_file=bcl2fastq2-v2-20-software-guide-15051736-03.pdf
    
      8
    
      9pkgname=bcl2fastq-bin
    
      10pkgver="${_pkg_ver}"."${_pkg_build}"
    
      11pkgrel=4
    
      12pkgdesc="Demultiplexes data and converts BCL files generated by Illumina sequencers to FASTQ for downstream analysis"
    
      13arch=('x86_64')
    
      14url=https://support.illumina.com/downloads/bcl2fastq-conversion-software-v"${_eula_ver}".html
    
      15license=('custom:illumina')
    
      16provides=('bcl2fastq')
    
      17conflicts=('bcl2fastq')
    
      18# Illumina no longer offers a public direct-download URL for the v2.20 archive
    
      19# (it is gated behind a login). This sources a byte-identical copy from the
    
      20# Internet Archive -- verified by the sha256sum below -- so the package builds
    
      21# unattended. Original (login-gated) download page:
    
      22#   https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
    
      23source=(
    
      24  https://archive.org/download/bcl2fastq2-v"${_pkg_ver//./-}"-linux-x86-64/bcl2fastq2-v"${_pkg_ver//./-}"-linux-x86-64.zip
    
      25  https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v"${_eula_ver}"-eula.pdf
    
      26  https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/"${_guide_file}"
    
      27)
    
      28sha256sums=(
    
      29  '3744bc1c02fff1dd17d18c8e8b8b2cc2405b37d7d248b8889f4f8a8fc220b434'
    
      30  '0a8236fad01c86f72d43247606c7f6c029cebdedf23f4bcb691367602bd061de'
    
      31  '8e6bf9029282096470da3c5a2b427ffe12ab5082b5c3b797c707ff44422eab79'
    
      32)
    
      33
    
      34prepare() {
    
      35  echo 'Download of this software requires agreement with EULA at:'
    
      36  echo "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v${_eula_ver}-eula.pdf"
    
      37}
    
      38
    
      39build() {
    
      40  mkdir -p "${srcdir}"/"${pkgname}"-"${_pkg_ver}" && cd "$_"
    
      41  mv ../bcl2fastq2-v"${_pkg_ver}"."${_pkg_build}"-Linux-x86_64.rpm ./
    
      42  bsdtar -xf bcl2fastq2-v"${_pkg_ver}"."${_pkg_build}"-Linux-x86_64.rpm
    
      43}
    
      44
    
      45package() {
    
      46  install -Dm644 \
    
      47    "${srcdir}"/bcl2fastq2-v"${_eula_ver}"-eula.pdf \
    
      48    "${pkgdir}"/usr/share/licenses/bcl2fastq/bcl2fastq2-v"${_eula_ver}"-eula.pdf
    
      49
    
      50  install -Dm644 \
    
      51    "${srcdir}"/"${_guide_file}" \
    
      52    "${pkgdir}"/usr/share/doc/bcl2fastq/"${_guide_file}"
    
      53
    
      54  cd "${srcdir}"/"${pkgname}"-"${_pkg_ver}"
    
      55  install -Dm644 usr/local/share/COPYRIGHT "${pkgdir}"/usr/share/licenses/bcl2fastq/COPYRIGHT
    
      56  install -Dm644 usr/local/share/Changes "${pkgdir}"/usr/share/licenses/bcl2fastq/Changes
    
      57  install -Dm755 usr/local/bin/bcl2fastq "${pkgdir}"/usr/bin/bcl2fastq
    
      58}
    
      59

Scan history

Scanned at (UTC)	Severity	Rules
2026-08-03 00:08:14	LOW	2
2026-08-02 00:16:08	LOW	2
2026-08-01 00:11:18	LOW	2
2026-07-31 00:14:10	LOW	2
2026-07-30 00:17:23	LOW	2
2026-07-29 00:25:53	LOW	2
2026-07-28 00:07:28	LOW	2
2026-07-27 00:24:32	LOW	2
2026-07-26 00:07:32	LOW	2
2026-07-25 00:13:44	LOW	2
2026-07-24 00:02:28	LOW	2
2026-07-23 00:14:47	LOW	2
2026-07-22 00:29:32	LOW	2
2026-07-21 00:24:15	LOW	2
2026-07-20 00:19:49	LOW	2
2026-07-19 00:17:08	LOW	2
2026-07-18 00:14:48	LOW	2
2026-07-17 00:06:16	LOW	2
2026-07-16 00:05:41	LOW	2
2026-07-15 00:09:25	LOW	2