diff --git a/Program_Licenses.md b/Program_Licenses.md index a8c6d80db..bcd0c34d2 100644 --- a/Program_Licenses.md +++ b/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 | diff --git a/README.md b/README.md index 2d0a05d6d..4ce1f517e 100644 --- a/README.md +++ b/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/)
[![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 | | [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/0.2.0/Dockerfile b/skani/0.2.0/Dockerfile new file mode 100644 index 000000000..95bba6d94 --- /dev/null +++ b/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 \ No newline at end of file diff --git a/skani/0.2.0/README.md b/skani/0.2.0/README.md new file mode 100644 index 000000000..439299d7d --- /dev/null +++ b/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/* +```