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add skani 0.2.1 #772

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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -228,7 +228,7 @@ To learn more about the docker pull rate limits and the open source software pro
| [Shovill-se](https://hub.docker.com/r/staphb/shovill-se/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/shovill-se)](https://hub.docker.com/r/staphb/shovill-se) | <ul><li>1.1.0</li></ul> | https://github.com/rpetit3/shovill/tree/v1.1.0se |
| [SISTR](https://hub.docker.com/r/staphb/sistr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | <ul><li>1.0.2</li><li>1.1.1</li></ul> | https://github.com/phac-nml/sistr_cmd |
| [SKA](https://hub.docker.com/r/staphb/ska/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska)](https://hub.docker.com/r/staphb/ska) | <ul><li>1.0</li></ul> | https://github.com/simonrharris/SKA |
| [skani](https://github.com/bluenote-1577/skani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/ska) | <ul><li>[0.2.0](./skani/0.2.0)</li></ul> | https://github.com/bluenote-1577/skani |
| [skani](https://github.com/bluenote-1577/skani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/skani) | <ul><li>[0.2.0](./skani/0.2.0)</li><li>[0.2.1](./skani/0.2.1)</li></ul> | https://github.com/bluenote-1577/skani |
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Good catch on finding the link typo!

| [SKESA](https://hub.docker.com/r/staphb/skesa) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/skesa)](https://hub.docker.com/r/staphb/skesa) | <ul><li>2.3.0</li><li>2.4.0 (`gfa_connector` & `kmercounter` included)</li></ul> | https://github.com/ncbi/SKESA |
| [Smalt](https://hub.docker.com/r/staphb/smalt) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/smalt)](https://hub.docker.com/r/staphb/smalt) | <ul><li>0.7.6</li></ul> | https://www.sanger.ac.uk/tool/smalt-0/ |
| [snpeff](https://hub.docker.com/r/staphb/snpeff) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/snpeff)](https://hub.docker.com/r/staphb/snpeff) | <ul><li>5.1</li></ul> | https://pcingola.github.io/SnpEff |
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47 changes: 47 additions & 0 deletions skani/0.2.1/Dockerfile
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ARG SKANI_VER="0.2.1"

## Builder ##
FROM rust:1.67 as builder

ARG SKANI_VER

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

## App ##
FROM ubuntu:jammy as app

ARG SKANI_VER

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]"

# copy app from builder stage
COPY --from=builder /root/.cargo/bin/skani /usr/local/bin/skani

# default run command
CMD skani -h

# singularity compatibility
ENV LC_ALL=C

WORKDIR /data

## Test ##
FROM app as test

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

RUN skani dist e.coli-EC590.fasta e.coli-K12.fasta
69 changes: 69 additions & 0 deletions skani/0.2.1/README.md
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@@ -0,0 +1,69 @@
<!--
Please edit this readme with some basic information about the tool and how to use this container.
- Include information about databases and additional files that are included.
- Keep it short - you don't need to recreate the documentation from the creators.
- Do not just copy and paste the readme or help for the tool.
-->

# skani container

Main tool: [skani](https://github.com/bluenote-1577/skani)

Code repository: https://github.com/bluenote-1577/skani

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%.

Additional information:

This container does not contain any database or reference genome.

Full documentation: https://github.com/bluenote-1577/skani/wiki

## Example Usage

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/*
```


<!-- Example README
# pasty container

Main tool: [pasty](https://github.com/rpetit3/pasty)

Code repository: https://github.com/rpetit3/pasty

Additional tools:
- ncbi-blast+: 2.12.0
- python: 3.10.6

Basic information on how to use this tool:
- executable: pasty
- help: --help
- version: --version
- description: "A tool easily taken advantage of for in silico serogrouping of Pseudomonas aeruginosa isolates from genome assemblies"

Additional information:

Full documentation: [https://github.com/rpetit3/pasty](https://github.com/rpetit3/pasty)

## Example Usage

```bash
pasty --assembly /pasty-1.0.2/test/O1-GCF_000504045.fna.gz --prefix O1-GCF_000504045
```
-->