Merge pull request #893 from Kincekara/ska2

adds ska2

Program_Licenses.md

@@ -146,6 +146,7 @@ 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 |
+| SKA2 | Apache 2.0 | https://github.com/bacpop/ska.rust/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/ |

README.md

@@ -252,6 +252,7 @@ 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 |
+| [SKA2](https://hub.docker.com/r/staphb/ska2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ska2)](https://hub.docker.com/r/staphb/ska2) | <ul><li>[0.3.6](./ska2/0.3.6/)</li></ul> | https://github.com/bacpop/ska.rust |
 | [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/ |

ska2/0.3.6/Dockerfile

@@ -0,0 +1,46 @@
+FROM ubuntu:jammy as app
+
+ARG SKA2_VER="0.3.6"
+
+LABEL base.image="ubuntu:jammy"
+LABEL dockerfile.version="1"
+LABEL software="SKA2"
+LABEL software.version="${SKA2_VER}"
+LABEL description="A reimplementation of the SKA package in the rust language"
+LABEL website="https://github.com/bacpop/ska.rust"
+LABEL license="https://github.com/bacpop/ska.rust/blob/master/LICENSE"
+LABEL maintainer="Kutluhan Incekara"
+LABEL maintainer.email="[email protected]"
+
+RUN apt-get update && apt-get install --no-install-recommends -y \
+    wget &&\
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+RUN wget --no-check-certificate https://github.com/bacpop/ska.rust/releases/download/v${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
+
+
+

ska2/0.3.6/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
+```