Fix TileDB-VCF installation instructions

- Correct installation method: Docker images, not pip packages
- Update examples to show Docker container usage
- Based on actual TileDB-VCF repository documentation
This commit is contained in:
Jeremy Leipzig
2026-02-24 10:02:34 -07:00
parent 3c98f0cada
commit 18ecbc3b30

View File

@@ -75,50 +75,58 @@ Use **open source TileDB-VCF** (this skill) when:
## Quick Start
### Installation
```bash
# Install from conda-forge
conda install -c conda-forge tiledbvcf-py
# Or from PyPI
pip install tiledbvcf
TileDB-VCF is distributed as Docker images, not pip packages:
```bash
# Pull Docker images
docker pull tiledb/tiledbvcf-py # Python interface
docker pull tiledb/tiledbvcf-cli # Command-line interface
# Or build from source
git clone https://github.com/TileDB-Inc/TileDB-VCF.git
cd TileDB-VCF
# See documentation for build instructions
```
### Basic Examples
**Create and populate a dataset:**
```python
import tiledbvcf
**Create and populate a dataset (via Docker):**
```bash
# Create dataset
docker run --rm -v $PWD:/data -u "$(id -u):$(id -g)" \
tiledb/tiledbvcf-cli tiledbvcf create -u my_dataset
# Create a new dataset
ds = tiledbvcf.Dataset(uri="my_dataset", mode="w",
cfg=tiledbvcf.ReadConfig(memory_budget=1024))
# Ingest VCF files (can be run incrementally)
ds.ingest_samples(["sample1.vcf.gz", "sample2.vcf.gz"])
# Ingest VCF files
docker run --rm -v $PWD:/data -u "$(id -u):$(id -g)" \
tiledb/tiledbvcf-cli tiledbvcf store \
-u my_dataset --samples sample1.vcf.gz,sample2.vcf.gz
```
**Query variant data:**
**Query variant data (Python in Docker):**
```python
# Inside tiledb/tiledbvcf-py container
import tiledbvcf
# Open existing dataset for reading
ds = tiledbvcf.Dataset(uri="my_dataset", mode="r")
# Query specific regions and samples
df = ds.read(
attrs=["sample_name", "pos_start", "pos_end", "alleles", "fmt_GT"],
regions=["chr1:1000000-2000000", "chr2:500000-1500000"],
samples=["sample1", "sample2", "sample3"]
regions=["chr1:1000000-2000000"],
samples=["sample1", "sample2"]
)
print(df.head())
```
**Export to VCF:**
```python
# Export query results as VCF
ds.export_bcf(
uri="output.bcf",
regions=["chr1:1000000-2000000"],
samples=["sample1", "sample2"]
)
**Export to VCF (via CLI):**
```bash
# Export query results as BCF
docker run --rm -v $PWD:/data \
tiledb/tiledbvcf-cli tiledbvcf export \
--uri my_dataset --regions "chr1:1000000-2000000" \
--sample-names "sample1,sample2" --output-format bcf
```
## Core Capabilities