Add LisSero 0.4.10 container #1724
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| FROM mambaorg/micromamba:2.8.1-ubuntu24.04 AS app | ||
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| ARG LISSERO_VERSION="0.4.10" | ||
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| USER root | ||
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| WORKDIR / | ||
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| LABEL base.image="mambaorg/micromamba:2.8.1-ubuntu24.04" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="LisSero" | ||
| LABEL software.version="${LISSERO_VERSION}" | ||
| LABEL description="In silico serogroup typing of Listeria monocytogenes" | ||
| LABEL website="https://github.com/MDU-PHL/LisSero" | ||
| LABEL license="https://github.com/MDU-PHL/LisSero/blob/master/LICENSE" | ||
| LABEL maintainer="Arnold Rodriguez" | ||
| LABEL maintainer.email="arnold.rodriguezhilario@flhealth.gov" | ||
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| # lissero pulls python and blast; procps-ng provides ps; wget is used by the test stage | ||
| RUN micromamba install --yes --name base -c conda-forge -c bioconda \ | ||
| lissero=${LISSERO_VERSION} procps-ng wget && \ | ||
| micromamba clean -a -f -y | ||
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| ENV PATH="/opt/conda/bin/:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
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| CMD [ "lissero", "--help" ] | ||
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| WORKDIR /data | ||
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| ## Test ## | ||
| FROM app AS test | ||
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| # serotype 4b reference (F2365, GCF_000008285.1); expect serogroup "4b, 4d, 4e" | ||
| RUN wget -q "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/285/GCF_000008285.1_ASM828v1/GCF_000008285.1_ASM828v1_genomic.fna.gz" && \ | ||
| gunzip GCF_000008285.1_ASM828v1_genomic.fna.gz && \ | ||
| lissero GCF_000008285.1_ASM828v1_genomic.fna | tee lissero_test.tsv && \ | ||
| grep "4b, 4d, 4e" lissero_test.tsv | ||
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| RUN lissero --version && \ | ||
| blastn -version | ||
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| RUN micromamba list -n base | ||
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| # LisSero container | ||
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| Main tool: [LisSero](https://github.com/MDU-PHL/LisSero) | ||
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| Code repository: https://github.com/MDU-PHL/LisSero | ||
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| <details> | ||
| <summary>Additional tools installed via micromamba:</summary> | ||
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| ``` | ||
| Name Version Build Channel | ||
| ──────────────────────────────────────────────────────────────────────────── | ||
| _openmp_mutex 4.5 20_gnu conda-forge | ||
| biopython 1.87 py314h5bd0f2a_0 conda-forge | ||
| blast 2.17.0 h66d330f_0 bioconda | ||
| bzip2 1.0.8 hda65f42_9 conda-forge | ||
| c-ares 1.34.6 hb03c661_0 conda-forge | ||
| ca-certificates 2026.6.17 hbd8a1cb_0 conda-forge | ||
| click 8.4.1 pyhc90fa1f_0 conda-forge | ||
| curl 8.21.0 hcf29cc6_0 conda-forge | ||
| entrez-direct 24.0 he881be0_0 bioconda | ||
| icu 78.3 h33c6efd_0 conda-forge | ||
| ispcr 33 h7b50bb2_6 bioconda | ||
| keyutils 1.6.3 hb9d3cd8_0 conda-forge | ||
| krb5 1.22.2 hbde042b_1 conda-forge | ||
| ld_impl_linux-64 2.45.1 default_hbd61a6d_102 conda-forge | ||
| libblas 3.11.0 8_h4a7cf45_openblas conda-forge | ||
| libcblas 3.11.0 8_h0358290_openblas conda-forge | ||
| libcurl 8.21.0 hcf29cc6_0 conda-forge | ||
| libedit 3.1.20250104 pl5321h7949ede_0 conda-forge | ||
| libev 4.33 hd590300_2 conda-forge | ||
| libexpat 2.8.1 hecca717_1 conda-forge | ||
| libffi 3.5.2 h3435931_0 conda-forge | ||
| libgcc 15.2.0 he0feb66_19 conda-forge | ||
| libgcc-ng 15.2.0 h69a702a_19 conda-forge | ||
| libgfortran 15.2.0 h69a702a_19 conda-forge | ||
| libgfortran5 15.2.0 h68bc16d_19 conda-forge | ||
| libgomp 15.2.0 he0feb66_19 conda-forge | ||
| libidn2 2.3.8 hfac485b_1 conda-forge | ||
| liblapack 3.11.0 8_h47877c9_openblas conda-forge | ||
| liblzma 5.8.3 hb03c661_0 conda-forge | ||
| libmpdec 4.0.0 hb03c661_1 conda-forge | ||
| libnghttp2 1.68.1 h877daf1_0 conda-forge | ||
| libopenblas 0.3.33 pthreads_h94d23a6_0 conda-forge | ||
| libsqlite 3.53.2 hf4e2dac_1 conda-forge | ||
| libssh2 1.11.1 hcf80075_0 conda-forge | ||
| libstdcxx 15.2.0 h934c35e_19 conda-forge | ||
| libunistring 0.9.10 h7f98852_0 conda-forge | ||
| libuuid 2.42.2 h5347b49_0 conda-forge | ||
| libxcrypt 4.4.36 hd590300_1 conda-forge | ||
| libzlib 1.3.2 h25fd6f3_2 conda-forge | ||
| lissero 0.4.10 pyhdfd78af_0 bioconda | ||
| loguru 0.7.3 pyh707e725_0 conda-forge | ||
| ncbi-vdb 3.4.1 hd63eeec_0 bioconda | ||
| ncurses 6.6 hdb14827_0 conda-forge | ||
| numpy 2.5.0 py314h2b28147_0 conda-forge | ||
| openssl 3.6.3 h35e630c_0 conda-forge | ||
| pcre2 10.47 haa7fec5_0 conda-forge | ||
| perl 5.32.1 7_hd590300_perl5 conda-forge | ||
| perl-archive-tar 3.12 pl5321hdfd78af_0 bioconda | ||
| perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge | ||
| perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge | ||
| perl-compress-raw-bzip2 2.214 pl5321hda65f42_0 conda-forge | ||
| perl-compress-raw-zlib 2.214 pl5321h4dac143_0 conda-forge | ||
| perl-encode 3.24 pl5321hb03c661_0 conda-forge | ||
| perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge | ||
| perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge | ||
| perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge | ||
| perl-io-compress 2.216 pl5321h503566f_0 bioconda | ||
| perl-io-zlib 1.15 pl5321hdfd78af_1 bioconda | ||
| perl-json 4.11 pl5321hdfd78af_0 bioconda | ||
| perl-json-xs 4.04 pl5321h9948957_0 bioconda | ||
| perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda | ||
| perl-list-moreutils-xs 0.430 pl5321h7b50bb2_5 bioconda | ||
| perl-parent 0.243 pl5321hd8ed1ab_0 conda-forge | ||
| perl-pathtools 3.75 pl5321hb9d3cd8_2 conda-forge | ||
| perl-scalar-list-utils 1.70 pl5321hb03c661_0 conda-forge | ||
| perl-storable 3.15 pl5321hb9d3cd8_2 conda-forge | ||
| perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda | ||
| procps-ng 4.0.6 h18c060e_0 conda-forge | ||
| python 3.14.6 habeac84_100_cp314 conda-forge | ||
| python_abi 3.14 8_cp314 conda-forge | ||
| readline 8.3 h853b02a_0 conda-forge | ||
| tk 8.6.13 noxft_h366c992_103 conda-forge | ||
| tzdata 2025c hc9c84f9_1 conda-forge | ||
| wget 1.25.0 h653f8fd_1 conda-forge | ||
| zlib 1.3.2 h25fd6f3_2 conda-forge | ||
| zstd 1.5.7 hb78ec9c_6 conda-forge | ||
| ``` | ||
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| </details> | ||
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Contributor
There was a problem hiding this comment. Can you add a section in the readme that lists all of the packages installed via micromamba? Specifically, I'm looking for the output of This is an example from the piranha image. It helps in troubleshooting issues. |
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| Basic information on how to use this tool: | ||
| - executable: lissero | ||
| - help: --help | ||
| - version: --version | ||
| - description: In silico serogroup prediction for Listeria monocytogenes from assembled genomes | ||
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| Additional information: | ||
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| LisSero infers the Listeria monocytogenes serogroup from an assembly by detecting the presence or absence of five markers with BLAST, following the Doumith et al. 2004 multiplex-PCR scheme (Differentiation of the major Listeria monocytogenes serovars by multiplex PCR. J Clin Microbiol 42(8):3819-22). The marker database is bundled with the tool, so no external download is required. | ||
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| Marker-to-serogroup logic (column order matches the output table): | ||
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| | Serogroup | prs | lmo0737 | lmo1118 | ORF2110 | ORF2819 | | ||
| |-----------|-----|---------|---------|---------|---------| | ||
| | 1/2a, 3a | + | + | - | - | - | | ||
| | 1/2b, 3b, 7 | + | - | - | - | + | | ||
| | 1/2c, 3c | + | + | + | - | - | | ||
| | 4b, 4d, 4e | + | - | - | + | + | | ||
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| A match below the default identity or coverage threshold (95% each) is reported as PARTIAL and treated as absent. An assembly with only prs detected is reported as Nontypable, which can indicate serotype 4a or 4c. | ||
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| Known behavior: the reference strain EGD-e (GCF_000196035.1, serotype 1/2a) types as 1/2c, 3c in silico. The lmo#### markers are named after EGD-e's own locus tags, so the lmo1118 marker matches EGD-e at full length and the 1/2c logic fires. This reflects the molecular scheme, not a LisSero error. Use a serotype 4b reference such as F2365 (GCF_000008285.1) as a clean control; it types as 4b, 4d, 4e. | ||
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| Full documentation: https://github.com/MDU-PHL/LisSero | ||
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| ## Example Usage | ||
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| ```bash | ||
| # serogroup one or more assemblies; results print as a tab-delimited table | ||
| lissero assembly1.fasta assembly2.fasta > lissero.tsv | ||
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| # adjust the identity and coverage thresholds (defaults are 95) | ||
| lissero --min_id 95 --min_cov 95 assembly.fasta | ||
| ``` | ||
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Can you add this line to the end of your file?
micromamba listwill list everything that was installed via micromamba and helps keep the tool-specific readme up-to-date.