技能 busco-phylogeny
📦
busco-phylogeny
内容修订 r2 高风险 ⚙️ 外部命令🌐 网络访问📁 文件系统访问
生成 BUSCO 系统基因组学工作流
从基因组组装进行系统基因组学分析需要许多工具、调度器脚本和质量检查。此技能指导 BUSCO 或 compleasm 直系同源基因提取、比对、修剪、树推断和方法报告。
支持: Claude Codex Code(CC)
安装前请停下并请求确认。
请审查安装计划，并在更改文件前获得用户明确同意。
使用我的智能体安装
将此请求复制给你的智能体，其中包含权威 Skill 页面和清单。
智能体请求
Review the Skillstore skill "busco-phylogeny" from https://skillstore.io/skills/brunoasm-busco-phylogeny.md and its manifest at https://skillstore.io/api/skills/brunoasm-busco-phylogeny/manifest. Verify the artifact. Stop and obtain explicit user consent before installing or changing files.你的智能体仍应展示其计划，并按安全策略请求必要确认。
Agent 可读资源
当 AI Agent、爬虫或脚本需要干净上下文，而不是读取完整页面时，请使用这些链接。
测试它
正在使用“busco-phylogeny”。 我有 24 个昆虫基因组组装，并且可以使用 SLURM 集群。
预期结果:
- 一份结构化工作流计划，包含必要问题、推荐的 BUSCO lineage、目录布局和调度器策略。
- 一系列生成的作业脚本，用于直系同源基因发现、QC、比对、修剪和树推断。
- 一份最终检查清单，列出预期的树文件、QC 报告和方法文本。
正在使用“busco-phylogeny”。 我知道分类单元，但还没有 NCBI 组装 accession。
预期结果:
- 一个引导式 NCBI 组装发现步骤，包含针对组装级别和 RefSeq 状态的选择标准。
- 一份 accession 收集计划，以及基因组下载和样本重命名的后续步骤。
正在使用“busco-phylogeny”。 检查我的系统基因组学脚本是否已准备好在集群上运行。
预期结果:
- 一份验证报告，涵盖工具选项、输入和输出连续性、资源请求以及已知调度器假设。
- 提交大型作业前需要应用的具体修正。
安全审计
高风险v9 • 2026/7/23 打开版本化报告
Most static matches are benign workflow syntax, documentation markup, fixed relative paths, or safe argument-list subprocess calls. Confirmed risks include eval-based command injection, unverified executable downloads, and predictable shared temporary directories. No prompt injection, credential collection, or data-exfiltration intent was found. Static review was capped at 400/549 representative findings; omitted static matches are unconfirmed, so automatic publishing stays disabled until manual review.
29
已扫描文件
8,659
分析行数
32
复核项
0
已忽略误报
已确认安全问题 (1)
高
Command Injection Through Eval
run_aliscore.sh concatenates user-controlled option values and an alignment basename into ALISCORE_CMD, then executes the string with eval. A crafted -o, -t, -w, -r, or filename value can run arbitrary shell commands.
The option parser directly appends positional values to a command string, and line 217 passes that string to eval. Shell metacharacters in those values are therefore interpreted as commands.
能力复核项 (32)
这些是真实的本地能力，对此技能可能是预期行为，因此需要复核，但不会按已确认恶意行为计分。
高
Hardcoded URL
GITHUB_BASE="https://raw.githubusercontent.com/brunoasm/my_claude_skills/main/phylo_from_buscos/scri
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
if wget -q https://github.com/PatrickKueck/AliCUT/raw/master/Aliscore_v.2.0/Aliscore.02.2.pl -O scri
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget -q https://github.com/PatrickKueck/AliCUT/raw/master/ALICUT_V2.3.1/ALICUT_V2.31.pl -O scripts/A
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget -q https://github.com/PatrickKueck/AliCUT/raw/master/Aliscore_v.2.0/Aliscore_module.pm -O scrip
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget https://raw.githubusercontent.com/PatrickKueck/AliCUT/master/Aliscore.02.2.pl
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget https://raw.githubusercontent.com/PatrickKueck/AliCUT/master/Aliscore_module.pm
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget https://raw.githubusercontent.com/PatrickKueck/AliCUT/master/ALICUT_V2.31.pl
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget https://raw.githubusercontent.com/PatrickKueck/FASconCAT-G/master/FASconCAT-G_v1.06.1.pl
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
高
Hardcoded URL
wget https://github.com/iqtree/iqtree2/releases/download/v2.3.6/iqtree-2.3.6-Linux-intel.tar.gz
The instructions download an executable archive or installer without a checksum or signature before installation or execution. Compromise of the hosted artifact would allow code execution in the user's environment.
高
Hardcoded URL
wget https://github.com/iqtree/iqtree2/releases/download/v2.3.6/iqtree-2.3.6-macOS-intel.tar.gz
The instructions download an executable archive or installer without a checksum or signature before installation or execution. Compromise of the hosted artifact would allow code execution in the user's environment.
高
Hardcoded URL
wget https://github.com/iqtree/iqtree2/releases/download/v2.3.6/iqtree-2.3.6-macOS-arm.tar.gz
The instructions download an executable archive or installer without a checksum or signature before installation or execution. Compromise of the hosted artifact would allow code execution in the user's environment.
高
Hardcoded URL
wget https://github.com/smirarab/ASTRAL/raw/master/Astral.5.7.8.zip
The instructions download an executable archive or installer without a checksum or signature before installation or execution. Compromise of the hosted artifact would allow code execution in the user's environment.
高
Hardcoded URL
wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
The instructions download an executable archive or installer without a checksum or signature before installation or execution. Compromise of the hosted artifact would allow code execution in the user's environment.
高
Hardcoded URL
wget https://raw.githubusercontent.com/PatrickKueck/FASconCAT-G/master/FASconCAT-G_v1.06.1.pl -O FAS
The instructions download executable Perl code from a repository path without a checksum or signature, then install or run it. A changed or compromised upstream artifact would execute with the user's privileges.
中
Temp directory access
mkdir -p /tmp/phylo_downloads
The installation example reuses a predictable shared /tmp directory instead of creating a private directory. This permits local collisions and precreation attacks on installation artifacts.
中
Temp directory access
cd /tmp/phylo_downloads
The installation example enters a predictable shared /tmp directory without checking ownership or permissions. Another local process can precreate that path and influence downloaded installation files.
中
Temp directory access
rm -rf /tmp/phylo_downloads
The installation example recursively deletes a fixed shared /tmp path. Concurrent runs or a preexisting directory can cause cross-run data loss, so a private mktemp directory is required.
中
Temp directory access
mkdir -p /tmp/phylo_downloads
The installation example reuses a predictable shared /tmp directory instead of creating a private directory. This permits local collisions and precreation attacks on installation artifacts.
中
Temp directory access
cd /tmp/phylo_downloads
The installation example enters a predictable shared /tmp directory without checking ownership or permissions. Another local process can precreate that path and influence downloaded installation files.
中
Temp directory access
rm -rf /tmp/phylo_downloads
The installation example recursively deletes a fixed shared /tmp path. Concurrent runs or a preexisting directory can cause cross-run data loss, so a private mktemp directory is required.
中
Temp directory access
mkdir -p /tmp/phylo_downloads
The installation example reuses a predictable shared /tmp directory instead of creating a private directory. This permits local collisions and precreation attacks on installation artifacts.
中
Temp directory access
cd /tmp/phylo_downloads
The installation example enters a predictable shared /tmp directory without checking ownership or permissions. Another local process can precreate that path and influence downloaded installation files.
中
Temp directory access
rm -rf /tmp/phylo_downloads
The installation example recursively deletes a fixed shared /tmp path. Concurrent runs or a preexisting directory can cause cross-run data loss, so a private mktemp directory is required.
中
Temp directory access
mkdir -p /tmp/phylo_downloads
The installation example reuses a predictable shared /tmp directory instead of creating a private directory. This permits local collisions and precreation attacks on installation artifacts.
中
Temp directory access
cd /tmp/phylo_downloads
The installation example enters a predictable shared /tmp directory without checking ownership or permissions. Another local process can precreate that path and influence downloaded installation files.
中
Temp directory access
rm -rf /tmp/phylo_downloads
The installation example recursively deletes a fixed shared /tmp path. Concurrent runs or a preexisting directory can cause cross-run data loss, so a private mktemp directory is required.
中
Temp directory access
mkdir -p /tmp/phylo_downloads
The installation example reuses a predictable shared /tmp directory instead of creating a private directory. This permits local collisions and precreation attacks on installation artifacts.
中
Temp directory access
cd /tmp/phylo_downloads
The installation example enters a predictable shared /tmp directory without checking ownership or permissions. Another local process can precreate that path and influence downloaded installation files.
中
Temp directory access
rm -rf /tmp/phylo_downloads
The installation example recursively deletes a fixed shared /tmp path. Concurrent runs or a preexisting directory can cause cross-run data loss, so a private mktemp directory is required.
中
Temp directory access
mkdir -p /tmp/phylo_downloads
The installation example reuses a predictable shared /tmp directory instead of creating a private directory. This permits local collisions and precreation attacks on installation artifacts.
中
Temp directory access
cd /tmp/phylo_downloads
The installation example enters a predictable shared /tmp directory without checking ownership or permissions. Another local process can precreate that path and influence downloaded installation files.
中
Temp directory access
rm -rf /tmp/phylo_downloads
The installation example recursively deletes a fixed shared /tmp path. Concurrent runs or a preexisting directory can cause cross-run data loss, so a private mktemp directory is required.
风险因素
⚙️ 外部命令 (50)
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🌐 网络访问 (33)
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📁 文件系统访问 (50)
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审计者: codex 查看审计历史 →
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分享版本化评估报告、中性徽章、嵌入卡片和引用。Skillstore 只报告证据，不判断该 Skill 是否安全。
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https://skillstore.io/skills/brunoasm-busco-phylogeny/audits/9?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_reportMarkdown 徽章
[](https://skillstore.io/skills/brunoasm-busco-phylogeny?utm_source=security_passport_badge)HTML 徽章
<a href="https://skillstore.io/skills/brunoasm-busco-phylogeny?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/brunoasm-busco-phylogeny/security.svg" alt="Skillstore security assessment" loading="lazy"></a>嵌入卡片
<iframe src="https://skillstore.io/embed/skills/brunoasm-busco-phylogeny.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>学术引用 (APA · BibTeX · CFF)
APA 引用
brunoasm. (2026). busco-phylogeny security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/brunoasm-busco-phylogeny/audits/9BibTeX 引用
@techreport{brunoasm-brunoasm-busco-phylogeny-2026,
author = {brunoasm},
title = {busco-phylogeny security audit report (audit version 9)},
institution = {Skillstore},
year = {2026},
number = {9},
url = {https://skillstore.io/skills/brunoasm-busco-phylogeny/audits/9},
note = {Author version unspecified}
}CITATION.cff
cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "busco-phylogeny security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
- name: "brunoasm"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/brunoasm-busco-phylogeny/audits/9"
identifiers:
- type: other
value: "skillstore:brunoasm-busco-phylogeny:audit:9"
description: "Skillstore immutable audit report identifier"
Skillstore 评分
评分依据 证据置信度: 中 77
架构
85
可维护性
87
内容
70
社区
74
规范符合性
你能构建什么
构建基因组系统发育树
创建从基因组组装到串联树和物种树结果的完整工作流。
准备集群作业
为 compleasm、比对、修剪和树推断步骤生成特定调度器脚本。
记录系统基因组学流水线
生成 QC 摘要、输出检查清单以及带工具引用的方法文本草稿。
试试这些提示
启动基础工作流
为我的本地基因组组装生成 BUSCO 系统基因组学工作流。先问我必要问题，然后推荐目录结构和初始设置步骤。
查找 NCBI 组装
帮我从 NCBI 查找目标分类单元的基因组组装，选择合适的 accession，并为 BUSCO 或 compleasm 系统发育分析做好准备。
创建调度器脚本
使用我的基因组数量、CPU 限制、内存、walltime 和 BUSCO lineage，为 compleasm、MAFFT 比对、修剪、IQ-TREE 和 ASTRAL 创建 SLURM 或 PBS 脚本。
优化并验证流水线
在我将计划的系统基因组学工作流提交到集群运行之前，审查其资源分配、路径连续性、工具选项、替换模型和缺失的验证检查。
最佳实践
- 在运行生成的脚本前，确认工具版本、调度器限制和 Conda 激活行为。
- 使用包含 accession 和物种信息的稳定样本名称，以便追踪树结果。
- 单独运行第一个 compleasm 作业，以便在并行作业前缓存 BUSCO lineage 数据库。
避免
- 在确认 lineage 数据库和环境设置前提交所有基因组作业。
- 使用模糊的样本名称，导致最终树标签难以追踪。
- 生成树之后跳过 QC 解读和方法文档编写。
常见问题
此技能会自动运行系统基因组学工具吗？
它主要生成并验证工作流脚本。用户在自己的本地、SLURM 或 PBS 环境中运行这些脚本。
它能使用 NCBI 基因组吗？
可以。它包含用于查找组装、下载基因组以及为树标签重命名文件的指导和辅助脚本。
它支持哪些直系同源基因工具？
它专注于 BUSCO 或 compleasm 单拷贝直系同源基因，然后将这些输出连接到比对和建树步骤。
它能创建集群作业脚本吗？
可以。它包含用于 SLURM、PBS 和本地执行的模板，并带有 CPU、内存、walltime、lineage 和位点数量的占位符。
它会选择最佳替换模型吗？
它会推荐模型集合并使用 IQ-TREE 模型选择，但用户应根据自己的分类单元和序列类型确认选择。
用户在运行脚本前应审查什么？
用户应检查路径、调度器账户设置、Conda 激活、CPU 和内存请求、工具版本以及所有下载的依赖项。
开发者详情
作者
brunoasm许可证
MIT
Skillstore 修订
r2
版本提示
作者未声明版本。
引用
a39a91716eadede5f4cdefd78178fed4e837a128
维护新鲜度
2026/7/24
使用量
9 次下载 · 227 次浏览