adding skani version 0.3.1 (#1471)

Author: erinyoung

README.md

@@ -312,7 +312,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.2](./build-files/sistr/1.0.2/)</li><li>[1.1.1](./build-files/sistr/1.1.1/)</li><li>[1.1.2](./build-files/sistr/1.1.2/)</li><li>[1.1.3](./build-files/sistr/1.1.3/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[1.0](./build-files/ska/1.0/)</li></ul> </details> | https://github.com/simonrharris/SKA |
 | [SKA2](https://hub.docker.com/r/staphb/ska2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | <details><summary>Click to see all versions</summary> <ul><li>[0.3.6](./build-files/ska2/0.3.6/)</li><li>[0.3.7](./build-files/ska2/0.3.7/)</li><li>[0.3.10](./build-files/ska2/0.3.10/)</li><li>[0.4.0](./build-files/ska2/0.4.0/)</li><li>[0.4.1](./build-files/ska2/0.4.1/)</li></ul> </details> | https://github.com/bacpop/ska.rust |
-| [skani](https://github.com/bluenote-1577/skani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/skani) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.0](./build-files/skani/0.2.0)</li><li>[0.2.1](./build-files/skani/0.2.1)</li><li>[0.2.2](./build-files/skani/0.2.2)</li><li>[0.3.0](./build-files/skani/0.3.0)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.0](./build-files/skani/0.2.0)</li><li>[0.2.1](./build-files/skani/0.2.1)</li><li>[0.2.2](./build-files/skani/0.2.2)</li><li>[0.3.0](./build-files/skani/0.3.0)</li><li>[0.3.1](./build-files/skani/0.3.1)</li></ul> </details> | https://github.com/bluenote-1577/skani |
 | [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) | <details><summary>Click to see all versions</summary> <ul><li>[2.3.0](./build-files/skesa/2.3.0/)</li><li>[2.4.0 (`gfa_connector` & `kmercounter` included)](./build-files/skesa/2.4.0/)</li><li>[skesa.2.4.0_saute.1.3.0_2 (also known as 2.5.1)](./build-files/skesa/skesa.2.4.0_saute.1.3.0_2/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[0.7.6](./build-files/smalt/0.7.6/)</li></ul> </details> | 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) | <details><summary>Click to see all versions</summary> <ul><li>[5.1](./build-files/snpeff/5.1/)</li><li>[5.2a](./build-files/snpeff/5.2a/)</li><li>[5.2f](./build-files/snpeff/5.2f/)</li></ul> </details> | https://pcingola.github.io/SnpEff |

build-files/skani/0.3.1/Dockerfile

@@ -0,0 +1,47 @@
+ARG SKANI_VER="0.3.1"
+
+## Builder ##
+FROM rust:1.90.0 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="kutluhan.incekara@ct.gov"
+
+# 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

build-files/skani/0.3.1/README.md

@@ -0,0 +1,33 @@
+# 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/*
+```