diff --git a/README.md b/README.md index 04974c66c..c7af3bf63 100644 --- a/README.md +++ b/README.md @@ -261,7 +261,7 @@ 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 | -| [SKA2](https://hub.docker.com/r/staphb/ska2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | | https://github.com/bacpop/ska.rust | +| [SKA2](https://hub.docker.com/r/staphb/ska2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | | https://github.com/bacpop/ska.rust | | [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/ | diff --git a/ska2/0.3.7/Dockerfile b/ska2/0.3.7/Dockerfile new file mode 100644 index 000000000..8d8e3fc7c --- /dev/null +++ b/ska2/0.3.7/Dockerfile @@ -0,0 +1,46 @@ +FROM ubuntu:jammy as app + +ARG SKA2_VER="0.3.7" + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="SKA2" +LABEL software.version="${SKA2_VER}" +LABEL description="A reimplementation of the SKA package in the rust language" +LABEL website="https://github.com/bacpop/ska.rust" +LABEL license="https://github.com/bacpop/ska.rust/blob/master/LICENSE" +LABEL maintainer="Kutluhan Incekara" +LABEL maintainer.email="kutluhan.incekara@ct.gov" + +RUN apt-get update && apt-get install --no-install-recommends -y \ + wget &&\ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget --no-check-certificate https://github.com/bacpop/ska.rust/releases/download/v${SKA2_VER}/ska-v${SKA2_VER}-ubuntu-latest-stable.tar.gz &&\ + tar -C /usr/local/bin -xvf ska-v${SKA2_VER}-ubuntu-latest-stable.tar.gz ska &&\ + rm ska-v${SKA2_VER}-ubuntu-latest-stable.tar.gz + +ENV LC_ALL=C + +CMD [ "ska", "-h" ] + +WORKDIR /data + +## Test ## +FROM app as test + +# force bash to avoid shell errors +SHELL ["/bin/bash", "-c"] + +# adapted from tutorial https://www.bacpop.org/guides/building_trees_with_ska/ +RUN wget --no-check-certificate https://zenodo.org/record/8172518/files/building_trees_with_ska.tar &&\ + tar -xvf building_trees_with_ska.tar assemblies/LA002.fa.gz assemblies/LA022.fa.gz assemblies/LA023.fa.gz assemblies/LA026.fa.gz &&\ + paste <(ls assemblies | sed 's/[.].*$//g') <(ls -d assemblies/*) > laos_ska_input.tsv + +RUN ska build -f laos_ska_input.tsv -k 31 -o laos_ska_index --threads 4 &&\ + ska align --min-freq 1 --filter no-filter laos_ska_index.skf -o laos_ska_alignment.aln --threads 4 &&\ + head -c 1000 laos_ska_alignment.aln &&\ + grep ">" laos_ska_alignment.aln + + + diff --git a/ska2/0.3.7/README.md b/ska2/0.3.7/README.md new file mode 100644 index 000000000..abf740604 --- /dev/null +++ b/ska2/0.3.7/README.md @@ -0,0 +1,24 @@ +# SKA2 container + +Main tool: [SKA2](https://github.com/bacpop/ska.rust) + +Code repository: https://github.com/bacpop/ska.rust + +Basic information on how to use this tool: +- executable: ska +- help: -h, --help +- version: -V, --version +- description: SKA2 is a reimplementation of the SKA package in the rust language. Split k-mer analysis (version 2) uses exact matching of split k-mer sequences to align closely related sequences, typically small haploid genomes such as bacteria and viruses. + +Full documentation: https://docs.rs/ska/latest/ska/ + +## Example Usage + +```bash +# Build from two input FASTA files with a k-mer size of 31 +ska build -o seqs -k 31 assemblies/seq1.fa assemblies/seq2.fa +# align +ska align --min-freq 1 --filter no-filter -o seqs seqs.skf +# map +ska map ref.fa seqs.skf -o ref_mapped.aln +```