Merge pull request #1126 from erinyoung/erin-emmtyper

updating the emmtyper blast database

README.md

@@ -158,7 +158,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [DSK](https://hub.docker.com/r/staphb/dsk) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/dsk)](https://hub.docker.com/r/staphb/dsk) | <ul><li>[0.0.100](./dsk/0.0.100/)</li><li>[2.3.3](./dsk/2.3.3/)</li></ul> | https://gatb.inria.fr/software/dsk/ |
 | [el_gato](https://hub.docker.com/r/staphb/elgato) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/elgato)](https://hub.docker.com/r/staphb/elgato) | <ul><li>[1.15.2](./elgato/1.15.2)</li><li>[1.18.2](./elgato/1.18.2)</li><li>[1.19.0](./elgato/1.19.0)</li><li>[1.20.0](./elgato/1.20.0)</li><li>[1.20.1](./elgato/1.20.1)</li></ul> | https://github.com/appliedbinf/el_gato |
 | [emboss](https://hub.docker.com/r/staphb/emboss) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emboss)](https://hub.docker.com/r/staphb/emboss) | <ul><li>6.6.0 (no version)</li></ul> | http://emboss.sourceforge.net |
-| [emmtyper](https://hub.docker.com/r/staphb/emmtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | <ul><li>0.2.0</li></ul> | https://github.com/MDU-PHL/emmtyper |
+| [emmtyper](https://hub.docker.com/r/staphb/emmtyper) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emmtyper)](https://hub.docker.com/r/staphb/emmtyper) | <ul><li>[0.2.0](./emmtyper/0.2.0/)</li><li>[0.2.0-2412](./emmtyper/0.2.0-2412/)</li></ul> | https://github.com/MDU-PHL/emmtyper |
 | [emm-typing-tool](https://hub.docker.com/r/staphb/emm-typing-tool) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/emm-typing-tool)](https://hub.docker.com/r/staphb/emm-typing-tool) | <ul><li>0.0.1 (no version)</li></ul> | https://github.com/phe-bioinformatics/emm-typing-tool |
 | [EToKi](https://hub.docker.com/r/staphb/etoki) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/etoki)](https://hub.docker.com/r/staphb/etoki) | <ul><li>1.2.1</li></ul> | https://github.com/zheminzhou/EToKi |
 | [FastANI](https://hub.docker.com/r/staphb/fastani) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/fastani)](https://hub.docker.com/r/staphb/fastani) | <ul><li>1.1</li><li>1.32</li><li>1.33</li><li>1.33 + RGDv2</li><li>[1.34](fastani/1.34)</li><li>[1.34 + RGDv2](fastani/1.34-RGDV2/)</li></ul> | https://github.com/ParBLiSS/FastANI |

emmtyper/0.2.0-2412/Dockerfile

@@ -0,0 +1,60 @@
+FROM mambaorg/micromamba:1.5.8 AS app
+
+# build and run as root users since micromamba image has 'mambauser' set as the $USER
+USER root
+# set workdir to default for building
+WORKDIR /
+
+ARG EMMTYPER_VER="0.2.0"
+
+LABEL base.image="mambaorg/micromamba:1.5.8"
+LABEL dockerfile.version="1"
+LABEL software="emmtyper"
+LABEL software.version=${EMMTYPER_VER}
+LABEL description="Conda environment for emmtyper. emmtyper is a command line tool for emm-typing of Streptococcus pyogenes using a de novo or complete assembly."
+LABEL website="https://github.com/MDU-PHL/emmtyper"
+LABEL license="GNU General Public License v3.0"
+LABEL license.url="https://github.com/MDU-PHL/emmtyper/blob/master/LICENSE"
+LABEL maintainer="Henry Kunerth"
+LABEL maintainer.email="[email protected]"
+
+# install dependencies; cleanup apt garbage
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    ca-certificates \
+    procps && \
+    apt-get autoclean && rm -rf /var/lib/apt/lists/*
+
+#install emmtyper and dependencies
+RUN micromamba create -n emmtyper -y -c conda-forge -c defaults -c bioconda emmtyper=${EMMTYPER_VER} && \
+    micromamba clean -a -f -y
+
+# set the environment
+ENV PATH="/opt/conda/envs/emmtyper/bin:/opt/conda/envs/env/bin:${PATH}" \
+    LC_ALL=C.UTF-8
+
+# overwriting the emmtyper database
+WORKDIR /opt/conda/envs/emmtyper/lib/python3.13/site-packages/emmtyper/db
+
+# removing original files and replacing with most-current fasta file
+RUN rm * && \
+    wget -q https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa && \
+    makeblastdb -in alltrimmed.tfa -dbtype nucl -out emm.fna
+
+CMD ["emmtyper",  "--help"]
+
+WORKDIR /data
+
+FROM app AS test
+
+WORKDIR /test
+
+RUN emmtyper --help && emmtyper --version
+
+RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/006/785/GCA_000006785.2_ASM678v2/GCA_000006785.2_ASM678v2_genomic.fna.gz && \
+	gunzip GCA_000006785.2_ASM678v2_genomic.fna.gz && \
+	mv GCA_000006785.2_ASM678v2_genomic.fna test_data.fasta
+
+RUN emmtyper test_data.fasta && \
+	emmtyper -w pcr test_data.fasta -o test_out && \
+	head test_out

emmtyper/0.2.0-2412/README.md

@@ -0,0 +1,36 @@
+# emmtyper container
+
+Main tool : [emmtyper](https://github.com/MDU-PHL/emmtyper)
+
+Code repository: https://github.com/MDU-PHL/emmtyper
+
+Basic information on how to use this tool:
+- executable: emmtyper
+- help: --help
+- version: --version
+- description: |
+
+'emmtyper' is a command line tool for emm-typing of _Streptococcus pyogenes_ using a _de novo_ or complete assembly.
+
+Additional information:
+
+This image uses the most up-to-date fasta file for emm typing by downloading from https://ftp.cdc.gov/pub/infectious_diseases/biotech/tsemm/alltrimmed.tfa. The out-of-date files are removed and overwritten at the time of building and deployment.
+
+Full documentation: https://github.com/MDU-PHL/emmtyper
+
+## Example Usage
+
+```bash
+# run emmtyper in BLAST (default) mode:
+
+emmtyper <file name(s)>.fasta -o <output_file>
+
+# or with output written in verbose format:
+
+emmtyper <file name(s)>.fasta -o <output_file> -f verbose
+
+# run emmtyper in PCR mode (useful for troubleshooting, see documentation)
+
+emmtyper -w pcr <file name(s)>.fasta -o <output_file_2> 
+
+```