Skill: djemec/bioskills (version 3.0.0)

--- name: bioskills description: "Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed." metadata: {"openclaw":{"requires":{"bins":["git"],"anyBins":["python3","Rscript"]},"os":["darwin","linux"],"emoji":"🧬"}} --- # bioSkills Installer Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis. ## Installation Run the bundled install script to download and install all bioSkills: ```bash bash scripts/install-bioskills.sh ``` Or install only specific categories: ```bash bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression" ``` ## What Gets Installed | Category Group | Categories | Skills | |----------------|-----------|--------| | Sequence & Alignment | sequence-io, sequence-manipulation, alignment, alignment-files, database-access | 40 | | Read Processing | read-qc, read-alignment | 11 | | RNA-seq & Expression | differential-expression, rna-quantification, expression-matrix | 14 | | Single-Cell & Spatial | single-cell, spatial-transcriptomics | 25 | | Variant Analysis | variant-calling, copy-number, phasing-imputation | 21 | | Epigenomics | chip-seq, atac-seq, methylation-analysis, hi-c-analysis | 25 | | Metagenomics & Microbiome | metagenomics, microbiome | 13 | | Genomics & Assembly | genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design | 29 | | Regulatory & Causal | gene-regulatory-networks, causal-genomics, rna-structure | 13 | | Temporal & Ecological | temporal-genomics, ecological-genomics | 11 | | Immunology & Clinical | immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics | 25 | | Specialized Omics | proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy | 36 | | RNA Biology | small-rna-seq, epitranscriptomics, clip-seq, ribo-seq | 20 | | Phylogenetics & Evolution | phylogenetics, population-genetics, comparative-genomics | 16 | | Structural & Systems | structural-biology, systems-biology | 11 | | Screens & Cytometry | crispr-screens, flow-cytometry, imaging-mass-cytometry | 22 | | Pathway & Integration | pathway-analysis, multi-omics-integration, restriction-analysis | 14 | | Infrastructure | data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing | 39 | | Workflows | End-to-end pipelines (FASTQ to results) | 40 | ## After Installation Once installed, skills are automatically triggered based on the task at hand. Example requests: - "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes" - "Call variants from this whole genome sequencing BAM file" - "Cluster my single-cell RNA-seq data and find marker genes" - "Predict the structure of this protein sequence" - "Run a metagenomics classification on these shotgun reads" ## Source GitHub: https://github.com/GPTomics/bioSkills ## Related Skills After installation, 425 individual skills become available across these categories: sequence-io, sequence-manipulation, database-access, alignment, alignment-files, variant-calling, phylogenetics, differential-expression, structural-biology, single-cell, pathway-analysis, restriction-analysis, methylation-analysis, chip-seq, metagenomics, long-read-sequencing, read-qc, read-alignment, rna-quantification, genome-assembly, genome-intervals, data-visualization, expression-matrix, copy-number, proteomics, flow-cytometry, population-genetics, multi-omics-integration, spatial-transcriptomics, machine-learning, workflow-management, microbiome, metabolomics, phasing-imputation, primer-design, hi-c-analysis, imaging-mass-cytometry, atac-seq, crispr-screens, reporting, experimental-design, clinical-databases, tcr-bcr-analysis, small-rna-seq, epitranscriptomics, clip-seq, ribo-seq, genome-engineering, systems-biology, epidemiological-genomics, immunoinformatics, comparative-genomics, alternative-splicing, chemoinformatics, liquid-biopsy, genome-annotation, gene-regulatory-networks, causal-genomics, rna-structure, temporal-genomics, ecological-genomics, workflows

path: scripts/install-bioskills.sh
content: #!/bin/bash
#
# Install all bioSkills to OpenClaw
# Bundled with the bioskills meta-skill for ClawHub distribution
#
# Usage:
#   bash install-bioskills.sh                              # Install all 425 skills
#   bash install-bioskills.sh --categories "single-cell,variant-calling"  # Selective
#   bash install-bioskills.sh --update                     # Only update changed skills
#   bash install-bioskills.sh --uninstall                  # Remove all bio-* skills

set -e

REPO_URL="https://github.com/GPTomics/bioSkills.git"
RELEASE_TAG="3.0"
EXPECTED_COMMIT="fae219d8cacb7be84b96b3a99122556c1a42a47b"
INSTALL_DIR="$HOME/.openclaw/bioskills-repo"
SKILLS_DIR="$HOME/.openclaw/skills"

RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
NC='\033[0m'

CATEGORY_FILTER=""
UPDATE_MODE=false
UNINSTALL_MODE=false
VERBOSE=false

print_usage() {
    echo "Usage: $0 [OPTIONS]"
    echo ""
    echo "Install bioSkills $RELEASE_TAG to OpenClaw"
    echo ""
    echo "Options:"
    echo "  --categories CATS     Install only specified categories (comma-separated)"
    echo "  --update              Only update skills that have changed"
    echo "  --uninstall           Remove all bio-* prefixed skills"
    echo "  --verbose             Show detailed output"
    echo "  --help                Show this help message"
}

while [[ $# -gt 0 ]]; do
    case $1 in
        --categories)
            if [[ -n "$2" && ! "$2" =~ ^-- ]]; then
                CATEGORY_FILTER=$(echo "$2" | tr -d ' ')
                shift
            else
                echo "Error: --categories requires a comma-separated list"
                exit 1
            fi
            shift
            ;;
        --update) UPDATE_MODE=true; shift ;;
        --uninstall) UNINSTALL_MODE=true; shift ;;
        --verbose|-v) VERBOSE=true; shift ;;
        --help|-h) print_usage; exit 0 ;;
        *) echo "Unknown option: $1"; print_usage; exit 1 ;;
    esac
done

if [ "$UNINSTALL_MODE" = true ]; then
    if [ ! -d "$SKILLS_DIR" ]; then
        echo "No skills directory found at: $SKILLS_DIR"
        exit 0
    fi
    echo "Removing bioSkills from: $SKILLS_DIR"
    removed=0
    for skill_dir in "$SKILLS_DIR"/bio-*; do
        if [ -d "$skill_dir" ]; then
            rm -rf "$skill_dir"
            removed=$((removed + 1))
        fi
    done
    echo "Removed $removed skills."
    [ -d "$INSTALL_DIR" ] && rm -rf "$INSTALL_DIR" && echo "Removed cached repository."
    exit 0
fi

if ! command -v git &>/dev/null; then
    echo -e "${RED}Error: git is required but not found${NC}"
    exit 1
fi

verify_commit() {
    local dir="$1"
    local actual_commit
    actual_commit=$(git -C "$dir" rev-parse HEAD 2>/dev/null)
    if [ "$actual_commit" != "$EXPECTED_COMMIT" ]; then
        echo -e "${RED}Error: Repository integrity check failed${NC}"
        echo "  Expected: $EXPECTED_COMMIT"
        echo "  Actual:   $actual_commit"
        return 1
    fi
    [ "$VERBOSE" = true ] && echo -e "  ${GREEN}Verified commit: ${EXPECTED_COMMIT:0:12}${NC}"
    return 0
}

echo "bioSkills installer (release $RELEASE_TAG)"
echo "==========================================="
echo ""

if [ -d "$INSTALL_DIR/.git" ] && verify_commit "$INSTALL_DIR" 2>/dev/null; then
    echo "Using cached repository (verified)..."
else
    echo "Cloning bioSkills release $RELEASE_TAG..."
    tmpdir=$(mktemp -d)
    if git clone --quiet --depth 1 --branch "$RELEASE_TAG" "$REPO_URL" "$tmpdir"; then
        if verify_commit "$tmpdir"; then
            rm -rf "$INSTALL_DIR"
            mkdir -p "$(dirname "$INSTALL_DIR")"
            mv "$tmpdir" "$INSTALL_DIR"
        else
            rm -rf "$tmpdir"
            exit 1
        fi
    else
        rm -rf "$tmpdir"
        echo -e "${RED}Error: Failed to clone repository${NC}"
        exit 1
    fi
fi

echo ""

EXTRA_ARGS=""
[ -n "$CATEGORY_FILTER" ] && EXTRA_ARGS="$EXTRA_ARGS --categories $CATEGORY_FILTER"
[ "$UPDATE_MODE" = true ] && EXTRA_ARGS="$EXTRA_ARGS --update"
[ "$VERBOSE" = true ] && EXTRA_ARGS="$EXTRA_ARGS --verbose"

if [ -f "$INSTALL_DIR/install-openclaw.sh" ]; then
    bash "$INSTALL_DIR/install-openclaw.sh" $EXTRA_ARGS
else
    echo -e "${RED}Error: install-openclaw.sh not found in repository${NC}"
    exit 1
fi


Security scan verdicts — ClawScan: clean | static analysis: clean | VirusTotal: clean | SkillSpector: clean (LOW)