Merge pull request #758 from Kincekara/skani-0.2.0

added skani

Program_Licenses.md

@@ -122,6 +122,7 @@ The licenses of the open-source software that is contained in these Docker image
 | Shovill | GNU GPLv3 | https://github.com/tseemann/shovill/blob/master/LICENSE |
 | SISTR | Apache 2.0 | https://github.com/phac-nml/sistr_cmd/blob/master/LICENSE |
 | SKA | MIT | https://github.com/simonrharris/SKA/blob/master/LICENSE |
+| skani | MIT | https://github.com/bluenote-1577/skani/blob/main/LICENSE |
 | SKESA | Public Domain | https://github.com/ncbi/SKESA/blob/master/LICENSE |
 | Smalt | GNU GPLv3 | https://www.sanger.ac.uk/tool/smalt-0/ |
 | SnpEff | MIT | https://github.com/pcingola/SnpEff/blob/master/LICENSE.md |

README.md

@@ -155,6 +155,7 @@ 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 |
 | [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/0.2.0/Dockerfile

@@ -0,0 +1,47 @@
+ARG SKANI_VER="0.2.0"
+
+## 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="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

skani/0.2.0/README.md

@@ -0,0 +1,23 @@
+# skani container
+
+Main tool : [skani](https://github.com/bluenote-1577/skani)
+
+Full documentation: https://github.com/bluenote-1577/skani/wiki
+
+skani is a program for calculating average nucleotide identity (ANI) from DNA sequences (contigs/MAGs/genomes) for ANI > ~80%.
+
+## 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/*
+```