Merge pull request #900 from Kincekara/kma

update kma

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/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/ivar)](https://hub.docker.com/r/staphb/ivar) | <ul><li>1.1</li><li>1.1 (+SARS-CoV2 reference)</li><li>1.2.1</li><li>1.2.1 (+SC2 ref)</li><li>1.2.2 (+SC2 ref and artic bedfiles)</li><li>1.3</li><li>1.3.1</li><li>1.3.2</li><li>1.4.1</li><li>1.4.2</li></ul> | https://github.com/andersen-lab/ivar |
 | [Kaptive](https://hub.docker.com/r/staphb/kaptive/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kaptive)](https://hub.docker.com/r/staphb/kaptive) | <ul><li>[2.0.0](./kaptive/2.0.0/)</li><li>[2.0.3](./kaptive/2.0.3/)</li><li>[2.0.5](./kaptive/2.0.5/)</li><li>[2.0.8](./kaptive/2.0.8/)</li></ul> | https://github.com/klebgenomics/Kaptive |
 | [Kleborate](https://hub.docker.com/r/staphb/kleborate/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kleborate)](https://hub.docker.com/r/staphb/kleborate) | <ul><li>[2.0.4](./kleborate/2.0.4/)</li><li>[2.1.0](./kleborate/2.1.0/)</li><li>[2.2.0](./kleborate/2.3.2/)</li><li>[2.3.2](./kleborate/2.3.2)</li><li>[2.3.2-2023-05](kleborate/2.3.2-2023-05/)</li><li>[2.4.1](kleborate/2.4.1/)</li></ul> | https://github.com/katholt/Kleborate/ <br/> https://github.com/katholt/Kaptive/ |
-| [kma](https://hub.docker.com/r/staphb/kma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | <ul><li>1.2.21</li><li>1.4.10 (no database)</li></ul> | https://bitbucket.org/genomicepidemiology/kma/ |
+| [kma](https://hub.docker.com/r/staphb/kma/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kma)](https://hub.docker.com/r/staphb/kma) | <ul><li>1.2.21</li><li>1.4.10 (no database)</li><li>[1.4.14](./kma/1.4.14/) (no database)</li></ul> | https://bitbucket.org/genomicepidemiology/kma/ |
 | [Kraken](https://hub.docker.com/r/staphb/kraken/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kraken)](https://hub.docker.com/r/staphb/kraken) | <ul><li>1.0</li><li>1.1.1</li><li>1.1.1 (no database)</li></ul> | https://github.com/DerrickWood/kraken |
 | [Kraken2](https://hub.docker.com/r/staphb/kraken2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/kraken2)](https://hub.docker.com/r/staphb/kraken2) | <ul><li>2.0.8-beta (no database)</li><li>2.0.8-beta (MiniKraken2_v1_8GB db)</li><li>2.0.8-beta_hv (human + virus db)</li><li>2.0.9-beta (no db)</li><li>2.0.9-beta (Minikraken v2 RefSeq: bacteria, archaea, viral, and human 8GB db)</li><li>2.1.0 (no db)</li><li>2.1.1 (no db)</li><li>2.1.2 (no db)</li><li>[2.1.3](kraken2/2.1.3/) (no db)</li></ul> | https://github.com/DerrickWood/kraken2 |
 | [KrakenUniq](https://hub.docker.com/r/staphb/krakenuniq/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/krakenuniq)](https://hub.docker.com/r/staphb/krakenuniq) | <ul><li>[1.0.4](./krakenuniq/1.0.4) (no database)</li></ul> | https://github.com/fbreitwieser/krakenuniq |

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="[email protected]"
+LABEL maintainer2="Kutluhan Incekara"
+LABEL maintainer2.email="[email protected]"
+
+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

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`
+```