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ARG SKANI_VER="0.2.2" | ||
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## Builder ## | ||
FROM rust:1.80.1 AS builder | ||
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ARG SKANI_VER | ||
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RUN wget https://github.com/bluenote-1577/skani/archive/refs/tags/v${SKANI_VER}.tar.gz &&\ | ||
tar -xvf v${SKANI_VER}.tar.gz &&\ | ||
cd skani-${SKANI_VER} &&\ | ||
cargo install --path . --root ~/.cargo &&\ | ||
chmod +x /root/.cargo/bin/skani | ||
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## App ## | ||
FROM ubuntu:jammy AS app | ||
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ARG SKANI_VER | ||
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LABEL base.image="ubuntu:jammy" | ||
LABEL dockerfile.version="1" | ||
LABEL software="skani" | ||
LABEL software.version=${SKANI_VER} | ||
LABEL description="skani is a program for calculating average nucleotide identity (ANI) from DNA sequences (contigs/MAGs/genomes) for ANI > ~80%." | ||
LABEL website="https://github.com/bluenote-1577/skani" | ||
LABEL license="https://github.com/bluenote-1577/skani/blob/main/LICENSE" | ||
LABEL maintainer="Kutluhan Incekara" | ||
LABEL maintainer.email="[email protected]" | ||
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# copy app from builder stage | ||
COPY --from=builder /root/.cargo/bin/skani /usr/local/bin/skani | ||
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# default run command | ||
CMD skani -h | ||
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# singularity compatibility | ||
ENV LC_ALL=C | ||
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WORKDIR /data | ||
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## Test ## | ||
FROM app AS test | ||
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RUN apt-get update && apt-get install -y wget &&\ | ||
wget https://github.com/bluenote-1577/skani/raw/v0.2.0/refs/e.coli-EC590.fasta &&\ | ||
wget https://github.com/bluenote-1577/skani/raw/v0.2.0/refs/e.coli-K12.fasta | ||
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RUN skani dist e.coli-EC590.fasta e.coli-K12.fasta |
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# skani container | ||
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Main tool: [skani](https://github.com/bluenote-1577/skani) | ||
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Code repository: https://github.com/bluenote-1577/skani | ||
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Basic information on how to use this tool: | ||
- executable: skani | ||
- help: -h, --help | ||
- version: -V, --version | ||
- description: skani is a program for calculating average nucleotide identity (ANI) from DNA sequences (contigs/MAGs/genomes) for ANI > ~80%. | ||
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Additional information: | ||
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This container does not contain any database or reference genome. | ||
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Full documentation: https://github.com/bluenote-1577/skani/wiki | ||
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## Example Usage | ||
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Quick ANI calculation: | ||
```bash | ||
skani dist genome1.fa genome2.fa | ||
``` | ||
Memory-efficient database search: | ||
```bash | ||
skani sketch genomes/* -o database | ||
skani search -d database query1.fa query2.fa ... | ||
``` | ||
All-to-all comparison: | ||
```bash | ||
skani triangle genomes/* | ||
``` |