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adding core-snp-filter version 0.2.0 (#1125)
* adding core-snp-filter version 0.2.0 * used variable for version
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| FROM ubuntu:jammy as app | ||
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| ARG CORESNPFILTER_VER="0.2.0" | ||
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| # 'LABEL' instructions tag the image with metadata that might be important to the user | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Core-SNP-filter" | ||
| LABEL software.version="${CORESNPFILTER_VER}" | ||
| LABEL description="This is a tool to filter sites (i.e. columns) in a FASTA-format whole-genome pseudo-alignment" | ||
| LABEL website="https://github.com/rrwick/Core-SNP-filter" | ||
| LABEL license="https://github.com/rrwick/Core-SNP-filter/blob/main/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="eriny@utah.gov" | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| WORKDIR /usr/local/bin | ||
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| RUN wget -q https://github.com/rrwick/Core-SNP-filter/releases/download/v${CORESNPFILTER_VER}/coresnpfilter-linux-x86_64-musl-v${CORESNPFILTER_VER}.tar.gz && \ | ||
| tar -vxf coresnpfilter-linux-x86_64-musl-v${CORESNPFILTER_VER}.tar.gz && \ | ||
| rm -rf coresnpfilter-linux-x86_64-musl-v${CORESNPFILTER_VER}.tar.gz | ||
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| ENV LC_ALL=C | ||
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| CMD [ "coresnpfilter", "--help" ] | ||
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| # 'WORKDIR' sets working directory | ||
| WORKDIR /data | ||
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| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
| ##### Step 2. Set up the testing stage. ##### | ||
| ##### The docker image is built to the 'test' stage before merging, but ##### | ||
| ##### the test stage (or any stage after 'app') will be lost. ##### | ||
| ##### ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ----- ##### | ||
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| # A second FROM insruction creates a new stage | ||
| FROM app as test | ||
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| # set working directory so that all test inputs & outputs are kept in /test | ||
| WORKDIR /test | ||
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| # print help and version info; check dependencies (not all software has these options available) | ||
| # Mostly this ensures the tool of choice is in path and is executable | ||
| RUN coresnpfilter --help && \ | ||
| coresnpfilter --version | ||
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| RUN wget -q https://github.com/rrwick/Core-SNP-filter/raw/refs/heads/main/demo.fasta.gz && \ | ||
| coresnpfilter -e -c 0.95 demo.fasta.gz > demo_core.fasta && \ | ||
| head demo_core.fasta |
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| # Core-SNP-filter container | ||
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| Main tool: [Core-SNP-filter](https://github.com/rrwick/Core-SNP-filter) | ||
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| Code repository: https://github.com/rrwick/Core-SNP-filter | ||
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| Basic information on how to use this tool: | ||
| - executable: coresnpfilter | ||
| - help: -h | ||
| - version: -V | ||
| - description: | | ||
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| > This is a tool to filter sites (i.e. columns) in a FASTA-format whole-genome pseudo-alignment based on: | ||
| > - Whether the site contains variation or not. | ||
| > - How conserved the site is, i.e. contains an unambiguous base in a sufficient fraction of the sequences. | ||
| Full documentation: https://github.com/rrwick/Core-SNP-filter | ||
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| ## Example Usage | ||
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| ```bash | ||
| # Exclude invariant sites: | ||
| coresnpfilter -e core.full.aln > filtered.aln | ||
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| # With a strict core threshold (same as Snippy's core.aln): | ||
| coresnpfilter -e -c 1.0 core.full.aln > filtered.aln | ||
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| # With a slightly more relaxed core threshold: | ||
| coresnpfilter -e -c 0.95 core.full.aln > filtered.aln | ||
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| # Use gzipped files to save disk space: | ||
| coresnpfilter -e -c 0.95 core.full.aln.gz | gzip > filtered.aln.gz | ||
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| # Running without any options will work, but the output will be the same as the input: | ||
| coresnpfilter core.full.aln > filtered.aln | ||
| ``` |