Summary
encode-toolkit v0.3.0 was classified as CRITICAL RISK with a risk score of 709. Sigil detected 62 findings across 500 files, covering phases including provenance, install hooks, code patterns, network exfiltration, obfuscation. Review the findings below before installing this package.
Package description: MCP server for querying and downloading ENCODE Project genomics data directly from Claude
v0.3.0
21 March 2026, 19:22 UTC
by Sigil Bot
Risk Score
709
Findings
62
Files Scanned
500
Provenance
Findings by Phase
Phase Ordering
Phases are ordered by criticality, with the most dangerous at the top. Click any phase header to expand or collapse its findings. Critical phases are expanded by default.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/PKG-INFO:804
- Make sure you restarted Claude Desktop after adding the config
- Verify `uvx` is installed: `pip install uv` or `curl -LsSf https://astral.sh/uv/install.sh | sh`
Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/README.md:771
- Make sure you restarted Claude Desktop after adding the config
- Verify `uvx` is installed: `pip install uv` or `curl -LsSf https://astral.sh/uv/install.sh | sh`
Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/index.js:39
"Or install uv for automatic management:\n" +
" curl -LsSf https://astral.sh/uv/install.sh | sh"
);Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/plugin/skills/bioinformatics-installer/SKILL.md:431
# Install Nextflow (requires Java 11+)
curl -s https://get.nextflow.io | bash
mv nextflow /usr/local/bin/Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/plugin/skills/bioinformatics-installer/SKILL.md:659
- **ARM Mac (M1/M2/M3) compatibility**: Many bioinformatics tools lack native ARM builds. Use `CONDA_SUBDIR=osx-64` or Rosetta 2 emulation for x86_64 packages. Some tools (samtools, BWA) have ARM-native builds.
- **Nextflow requires Java 11+**: Nextflow will not run on Java 8. Check `java -version` before running pipelines. Install with `curl -s https://get.nextflow.io | bash` for correct Java bundling.
- **Docker vs Singularity on HPC**: Most HPC clusters do not allow Docker (requires root). UsWhy was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/plugin/skills/bioinformatics-installer/scripts/install-nextflow.sh:41
echo "Downloading Nextflow..."
curl -s https://get.nextflow.io | bash
Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/plugin/skills/bioinformatics-installer/scripts/install-nextflow.sh:74
echo "Linux detected. Install Docker Engine:"
echo " curl -fsSL https://get.docker.com | sh"
echo " sudo usermod -aG docker \$USER"Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/plugin/skills/setup/SKILL.md:235
| "Server not found" | Claude not restarted after config change | Restart Claude Desktop / reload Claude Code |
| "uvx not found" | uv not installed | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
| Timeout errors | Slow connection or ENCODE API load | Retry; rate limit (10 req/sec) is handled automatically |Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/skills/bioinformatics-installer/SKILL.md:431
# Install Nextflow (requires Java 11+)
curl -s https://get.nextflow.io | bash
mv nextflow /usr/local/bin/Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/skills/bioinformatics-installer/SKILL.md:659
- **ARM Mac (M1/M2/M3) compatibility**: Many bioinformatics tools lack native ARM builds. Use `CONDA_SUBDIR=osx-64` or Rosetta 2 emulation for x86_64 packages. Some tools (samtools, BWA) have ARM-native builds.
- **Nextflow requires Java 11+**: Nextflow will not run on Java 8. Check `java -version` before running pipelines. Install with `curl -s https://get.nextflow.io | bash` for correct Java bundling.
- **Docker vs Singularity on HPC**: Most HPC clusters do not allow Docker (requires root). UsWhy was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/skills/bioinformatics-installer/scripts/install-nextflow.sh:41
echo "Downloading Nextflow..."
curl -s https://get.nextflow.io | bash
Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/skills/bioinformatics-installer/scripts/install-nextflow.sh:74
echo "Linux detected. Install Docker Engine:"
echo " curl -fsSL https://get.docker.com | sh"
echo " sudo usermod -aG docker \$USER"Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
install-makefile-curl
HIGHMakefile/script pipes remote content to shell
encode_toolkit-0.3.0/skills/setup/SKILL.md:235
| "Server not found" | Claude not restarted after config change | Restart Claude Desktop / reload Claude Code |
| "uvx not found" | uv not installed | `curl -LsSf https://astral.sh/uv/install.sh \| sh` |
| Timeout errors | Slow connection or ENCODE API load | Retry; rate limit (10 req/sec) is handled automatically |Why was this flagged?
A script or Makefile pipes content from a remote URL directly into a shell (curl | sh or wget | bash). This is inherently dangerous because the remote content can change at any time, and the command runs with the current user's permissions. Rated HIGH because it requires manual execution (unlike install hooks) but still executes arbitrary remote code.
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