diff --git a/README.md b/README.md index 10b460d9e..6dfb85b18 100644 --- a/README.md +++ b/README.md @@ -178,7 +178,7 @@ To learn more about the docker pull rate limits and the open source software pro | [iVar](https://hub.docker.com/r/staphb/ivar/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | | https://github.com/andersen-lab/ivar | | [Kaptive](https://hub.docker.com/r/staphb/kaptive/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | | https://github.com/klebgenomics/Kaptive | | [Kleborate](https://hub.docker.com/r/staphb/kleborate/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | | https://github.com/katholt/Kleborate/
https://github.com/katholt/Kaptive/ | -| [kma](https://hub.docker.com/r/staphb/kma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | | https://bitbucket.org/genomicepidemiology/kma/ | +| [kma](https://hub.docker.com/r/staphb/kma/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | | https://bitbucket.org/genomicepidemiology/kma/ | | [Kraken](https://hub.docker.com/r/staphb/kraken/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | | https://github.com/DerrickWood/kraken | | [Kraken2](https://hub.docker.com/r/staphb/kraken2/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | | https://github.com/DerrickWood/kraken2 | | [KrakenUniq](https://hub.docker.com/r/staphb/krakenuniq/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/krakenuniq)](https://hub.docker.com/r/staphb/krakenuniq) | | https://github.com/fbreitwieser/krakenuniq | diff --git a/kma/1.4.14/Dockerfile b/kma/1.4.14/Dockerfile new file mode 100644 index 000000000..feded7860 --- /dev/null +++ b/kma/1.4.14/Dockerfile @@ -0,0 +1,61 @@ +ARG KMA_VER="1.4.14" + +## Builder ## +FROM ubuntu:jammy as builder + +ARG KMA_VER + +RUN apt-get update && apt-get install -y --no-install-recommends \ + gcc \ + libz-dev \ + make \ + ca-certificates \ + git && \ + rm -rf /var/lib/apt/lists/* && apt-get autoclean + +RUN git clone -b ${KMA_VER} --single-branch https://bitbucket.org/genomicepidemiology/kma.git &&\ + cd kma &&\ + make &&\ + mv kma kma_index kma_shm kma_update /usr/local/bin/ + +## App ## +FROM ubuntu:jammy as app + +ARG KMA_VER + +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="kma" +LABEL software.version="$KMA_VER" +LABEL description="K-mer alignment of raw reads against a database" +LABEL website="https://bitbucket.org/genomicepidemiology/kma/src/master/" +LABEL license="https://bitbucket.org/genomicepidemiology/kma/src/master/" +LABEL license.type="Apache License, V2.0" +LABEL maintainer="Curtis Kapsak" +LABEL maintainer.email="kapsakcj@gmail.com" +LABEL maintainer2="Kutluhan Incekara" +LABEL maintainer2.email="kutluhan.incekara@ct.gov" + +COPY --from=builder /usr/local/bin/* /usr/local/bin/ + +ENV LC_ALL=C + +CMD ["kma", "-h"] + +WORKDIR /data + +## Test ## +FROM app as test + +RUN apt-get update && apt-get install -y --no-install-recommends wget + +# Downloads E.coli genome and runs kma index on it +RUN wget -q --no-check-certificate https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/224/845/GCA_012224845.2_ASM1222484v2/GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \ + gunzip GCA_012224845.2_ASM1222484v2_genomic.fna.gz && \ + kma index -i GCA_012224845.2_ASM1222484v2_genomic.fna -o database + +# Downloads read files and uses them for kma mapping against database; print kma version +RUN wget -q --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR690/006/SRR6903006/SRR6903006_1.fastq.gz && \ + wget -q --no-check-certificate ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR690/006/SRR6903006/SRR6903006_2.fastq.gz && \ + kma -ipe SRR6903006_1.fastq.gz SRR6903006_2.fastq.gz -o test_output -t_db database -tmp /tmp/ && \ + kma -v diff --git a/kma/1.4.14/README.md b/kma/1.4.14/README.md new file mode 100644 index 000000000..c2fc6c438 --- /dev/null +++ b/kma/1.4.14/README.md @@ -0,0 +1,25 @@ +# kma container + +Main tool : [kma](https://bitbucket.org/genomicepidemiology/kma/) + +Code repository: https://bitbucket.org/genomicepidemiology/kma/src/master/ + +Basic information on how to use this tool: +- executable: kma +- help: -h +- version: -v +- description: k-mer mapping of raw reads to a redundant database + +Full documentation: https://bitbucket.org/genomicepidemiology/kma/src/master/ + +## Example Usage + +```bash +# Database needs to be indexed to use kma for mapping: +kma index -i templates.fsa.gz -o database/name + +# kma mapping of paired and unpaired read files: +kma -ipe SRR13957123_*.fastq.gz -o test.output -t_db DB_name + +kma -i singleEndReads.fq.gz -ipe pairedEnd_*.fq.gz -o output/name -t_db database/name -1t1` +```