Merge pull request #772 from Kincekara/skani-update

add skani 0.2.1

README.md

@@ -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 |
 | [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 |

skani/0.2.1/Dockerfile

@@ -0,0 +1,47 @@
+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

skani/0.2.1/README.md

@@ -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
+``` 
+-->