From 39ac740339917c0228bbb7fc63e5d3fdf68a1b30 Mon Sep 17 00:00:00 2001 From: Kincekara Date: Wed, 25 Oct 2023 18:38:30 +0000 Subject: [PATCH] add skani 0.2.1 --- README.md | 2 +- skani/0.2.1/Dockerfile | 47 ++++++++++++++++++++++++++++ skani/0.2.1/README.md | 69 ++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 117 insertions(+), 1 deletion(-) create mode 100644 skani/0.2.1/Dockerfile create mode 100644 skani/0.2.1/README.md diff --git a/README.md b/README.md index c1f19bcfd..7b00f48fa 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/shovill-se)](https://hub.docker.com/r/staphb/shovill-se) | | https://github.com/rpetit3/shovill/tree/v1.1.0se | | [SISTR](https://hub.docker.com/r/staphb/sistr/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/sistr)](https://hub.docker.com/r/staphb/sistr) | | https://github.com/phac-nml/sistr_cmd | | [SKA](https://hub.docker.com/r/staphb/ska/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ska)](https://hub.docker.com/r/staphb/ska) | | https://github.com/simonrharris/SKA | -| [skani](https://github.com/bluenote-1577/skani)
[![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/ska) | | https://github.com/bluenote-1577/skani | +| [skani](https://github.com/bluenote-1577/skani)
[![docker pulls](https://badgen.net/docker/pulls/staphb/skani)](https://hub.docker.com/r/staphb/skani) | | https://github.com/bluenote-1577/skani | | [SKESA](https://hub.docker.com/r/staphb/skesa)
[![docker pulls](https://badgen.net/docker/pulls/staphb/skesa)](https://hub.docker.com/r/staphb/skesa) | | https://github.com/ncbi/SKESA | | [Smalt](https://hub.docker.com/r/staphb/smalt)
[![docker pulls](https://badgen.net/docker/pulls/staphb/smalt)](https://hub.docker.com/r/staphb/smalt) | | https://www.sanger.ac.uk/tool/smalt-0/ | | [snpeff](https://hub.docker.com/r/staphb/snpeff)
[![docker pulls](https://badgen.net/docker/pulls/staphb/snpeff)](https://hub.docker.com/r/staphb/snpeff) | | https://pcingola.github.io/SnpEff | diff --git a/skani/0.2.1/Dockerfile b/skani/0.2.1/Dockerfile new file mode 100644 index 000000000..f2aa93a60 --- /dev/null +++ b/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="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 \ No newline at end of file diff --git a/skani/0.2.1/README.md b/skani/0.2.1/README.md new file mode 100644 index 000000000..e0d986aef --- /dev/null +++ b/skani/0.2.1/README.md @@ -0,0 +1,69 @@ + + +# 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/* +``` + + +