Grades are a hygiene check, not a security guarantee.

Claude Code, Plugin

Sciagent Skills

197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy.

Compatibility: Portable across standard formats.

Grade B

Minor issues only, no Medium or High. Worth a quick look at the findings below before installing.

Graded by PlugVetRubric v2

Not a guarantee. A hygiene check of the source at the commit shown, not a security audit.

Rescanned at commit 82c862c094a4, unchanged since the check below.

NETWORK_NO_FIXED_HOST NETWORK_UNNAMED_HOST SECRETS_PATH_DOTENV PERMISSION_SHELL_DECLARED INSTALL_DOCUMENTED_INSTALLER SECRETS_ENV_READ

Why this grade

  • NETWORK_NO_FIXED_HOST Low

    Makes a network call whose host is not written as a fixed address.

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 36 wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2

  • NETWORK_UNNAMED_HOST Low

    Calls a fixed host that the description does not name.

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 36 wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2

  • SECRETS_PATH_DOTENV Low

    Mentions a .env file.

    scripts/blind_knowledge_test.py, line 18 Environment (.env file):

  • PERMISSION_SHELL_DECLARED Note

    Runs shell commands, and the manifest or description says so.

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 316 result = subprocess.run(

  • INSTALL_DOCUMENTED_INSTALLER Note

    Documentation shows an installer that pipes a download into a shell.

    CONTRIBUTING.md, line 42 curl -fsSL https://pixi.sh/install.sh | bash

  • SECRETS_ENV_READ Note

    Reads an environment variable whose name contains KEY, SECRET, TOKEN, PASSWORD or CREDENTIAL.

    skills/scientific-computing/pymatgen/SKILL.md, line 110 api_key = os.environ.get("PMG_MAPI_KEY", "your_key")

Any High, or two or more Medium findings, give D. One Medium gives C. Low findings or a security Note give B. Each code names a finding behind the letter.

Grades are a hygiene check of the source at the commit shown, on the date checked, not a security audit or a guarantee. The free directory grades are automated. Before release, a PlugVet engineer reviews every paid report and any grade we hold back, including all F grades, against the source code and the evidence we quote.

What was checked

Plain notes from the hygiene checks.

  • Permissions

    Note

    requests shell access. The manifest names this permission.

    PERMISSION_SHELL_DECLARED

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 316

    result = subprocess.run(

    skills/genomics-bioinformatics/biopython-sequence-analysis/SKILL.md, line 262

    subprocess.run(

    skills/genomics-bioinformatics/biopython-sequence-analysis/SKILL.md, line 268

    result = subprocess.run(

    Show more

    skills/genomics-bioinformatics/biopython-sequence-analysis/SKILL.md, line 459

    subprocess.run(

    skills/genomics-bioinformatics/homer-motif-analysis/SKILL.md, line 495

    result = subprocess.run(cmd, capture_output=True, text=True)

    skills/genomics-bioinformatics/rnaseq/featurecounts-rna-counting/SKILL.md, line 305

    result = subprocess.run(cmd, capture_output=True, text=True)

    skills/genomics-bioinformatics/variant/cnvkit-copy-number/SKILL.md, line 287

    subprocess.run(

    skills/genomics-bioinformatics/variant/gatk-variant-calling/SKILL.md, line 267

    result = subprocess.run(

  • Install and update

    Note

    The docs document an installer that pipes a download into a shell. README documents an installer that pipes a download into a shell.

    INSTALL_DOCUMENTED_INSTALLER

    CONTRIBUTING.md, line 42

    curl -fsSL https://pixi.sh/install.sh | bash

    README.md, line 180

    curl -fsSL https://pixi.sh/install.sh | bash

    skills/scientific-computing/nextflow-workflow-engine/SKILL.md, line 33

    curl -s https://get.nextflow.io | bash

  • Network

    Concern

    can reach ftp.ncbi.nlm.nih.gov. The description does not name that host. can reach ftp.ebi.ac.uk. The description does not name that host. can reach a host that is not written as a fixed address. can reach api.clinpgx.org. The description does not name that host. can reach cancer.sanger.ac.uk. The description does not name that host. can reach eutils.ncbi.nlm.nih.gov. The description does not name that host. can reach jaspar.elixir.no. The description does not name that host. can reach rest.kegg

    NETWORK_NO_FIXED_HOST NETWORK_UNNAMED_HOST

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 36

    wget https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.2.1/bwa-mem2-2.2.1_x64-linux.tar.bz2

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 130

    wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz

    skills/genomics-bioinformatics/alignment/bwa-mem2-dna-aligner/SKILL.md, line 135

    wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/GRCh38.primary_assembly.genome.fa.gz

    Show more

    skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 85

    for read in bam.fetch("chr1", 1000, 2000):

    skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 103

    for read in bam.fetch("chr1", 10000, 20000):

    skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 116

    for read in bam.fetch("chr1", 10000, 20000):

    skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 127

    for read in inbam.fetch("chr1", 10000, 20000):

    skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 172

    for record in vcf.fetch("chr1", 10000, 50000):

    skills/genomics-bioinformatics/alignment/pysam-genomic-files/SKILL.md, line 207

    seq = fasta.fetch("chr1", 10000, 10050)

    skills/genomics-bioinformatics/qc/fastp-fastq-preprocessing/SKILL.md, line 35

    wget https://github.com/OpenGene/fastp/releases/download/v0.24.0/fastp

    skills/genomics-bioinformatics/rnaseq/salmon-rna-quantification/SKILL.md, line 40

    wget https://github.com/COMBINE-lab/salmon/releases/download/v1.10.0/salmon-1.10.0_linux_x86_64.tar.gz

    skills/genomics-bioinformatics/variant/gatk-variant-calling/SKILL.md, line 33

    wget https://github.com/broadinstitute/gatk/releases/download/4.6.0.0/gatk-4.6.0.0.zip

  • Secrets

    Concern

    reads a credential or environment file.

    SECRETS_ENV_READ SECRETS_PATH_DOTENV

    scripts/blind_knowledge_test.py, line 18

    Environment (.env file):

    scripts/blind_knowledge_test.py, line 110

    """Load .env file from given path or search common locations."""

    skills/scientific-computing/pymatgen/SKILL.md, line 110

    api_key = os.environ.get("PMG_MAPI_KEY", "your_key")

    Show more

    scripts/blind_knowledge_test.py, line 116

    REPO_ROOT / ".env",

    scripts/blind_knowledge_test.py, line 117

    Path.home() / ".env",

    scripts/blind_knowledge_test.py, line 118

    Path.home() / "work" / ".env",

    scripts/blind_knowledge_test.py, line 119

    Path(".env"),

    scripts/blind_knowledge_test.py, line 124

    print(f"Loaded .env from {path}")

    scripts/blind_knowledge_test.py, line 128

    print("No .env file found; using existing environment variables")

    skills/scientific-computing/pymatgen/SKILL.md, line 173

    api_key = os.environ.get("PMG_MAPI_KEY", "your_key")

    skills/scientific-computing/pymatgen/SKILL.md, line 272

    api_key = os.environ.get("PMG_MAPI_KEY", "your_key")

    skills/scientific-computing/pymatgen/SKILL.md, line 373

    api_key = os.environ.get("PMG_MAPI_KEY", "your_key")

  • Agent instructions

    Pass

    No instruction to ignore earlier instructions or to hide a step.

  • Obfuscation

    Pass

    No encoded or minified payload found.

  • Licence

    Pass

    A licence file is present (LICENSE).

  • Maintainer activity

    Pass

    The latest commit is within the last 365 days.

Get the full report on this tool, £49

Note

Hygiene check of commit 82c862c094a4. requests shell access. The manifest names this permission. The docs document an installer that pipes a download into a shell. README documents an installer that pipes a download into a shell. can reach ftp.ncbi.nlm.nih.gov. The description does not name that host. can reach ftp.ebi.ac.uk. The description does not name that host. can reach a host that is not written as a fixed address. can reach api.clinpgx.org. The description does not name that host. can reach cancer.sanger.ac.uk. The description does not name that host. can reach eutils.ncbi.nlm.nih.gov. The description does not name that host. can reach jaspar.elixir.no. The description

Date and source

Date checked:

View source

github.com

Commit graded: 82c862c094a4a5ec6eeeeee039c8dd34cd8a92be

This link goes to the original host. PlugVet does not host or check what you download from there, and installing it is your own decision and risk.

Read how this letter is chosen