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adding table2asn version 1.29.324 #1511
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| ARG RELEASE_DATE="2025-09-16" | ||
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| FROM ubuntu:jammy AS app | ||
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| # The directory structure is by date as opposed to version. | ||
| # A list of software versions should be found at a location similar to https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/CURRENT/documentation/VERSIONS | ||
| ARG TABLE2ASN_VER="1.29.324" | ||
| ARG RELEASE_DATE | ||
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| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="NCBI's table2asn" | ||
| LABEL software.version="${TABLE2ASN_VER}" | ||
| LABEL description="Converts files of various formats to ASN.1" | ||
| LABEL website="https://www.ncbi.nlm.nih.gov/genbank/table2asn/" | ||
| LABEL license="unknown" | ||
| LABEL maintainer="Sage Wright" | ||
| LABEL maintainer.email="[email protected]" | ||
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| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| wget \ | ||
| ca-certificates \ | ||
| gzip \ | ||
| libidn12 \ | ||
| libsqlite3-0 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* && \ | ||
| ln -s /usr/lib/x86_64-linux-gnu/libidn.so.12 /usr/lib/x86_64-linux-gnu/libidn.so.11 | ||
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| WORKDIR /usr/local/bin | ||
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| ENV STAPHB_TOOLS="agp_validate \ | ||
| asn2all \ | ||
| asn2asn \ | ||
| asn2fasta \ | ||
| asn2flat \ | ||
| asn2fsa \ | ||
| asn2gb \ | ||
| asn2idx \ | ||
| asn2xml \ | ||
| asndisc \ | ||
| asnmacro \ | ||
| asnval \ | ||
| asnvalidate \ | ||
| gap_stats \ | ||
| gene2xml \ | ||
| insdseqget \ | ||
| sbtedit \ | ||
| sqn2agp \ | ||
| srcchk \ | ||
| table2asn " | ||
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| RUN for tool in ${STAPHB_TOOLS} ; do \ | ||
| echo "Downloading ${tool}" && \ | ||
| wget -q https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/${RELEASE_DATE}/by_program/${tool}/linux64.${tool}.gz && \ | ||
| gunzip linux64.${tool}.gz && \ | ||
| mv linux64.${tool} ${tool} && \ | ||
| chmod +x ${tool} ; done | ||
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| ENV LC_ALL=C | ||
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| CMD ["table2asn", "-help"] | ||
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| WORKDIR /data | ||
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| FROM app AS test | ||
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| ARG RELEASE_DATE | ||
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| # NOTE: Not all of these tools support the '-help' or '-version flag' | ||
| # This ensures that all tools are in $PATH and executable | ||
| RUN for tool in ${STAPHB_TOOLS} ; do echo "Checking ${tool}" && ${tool} -help && ${tool} -version ; done | ||
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| WORKDIR /test | ||
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| RUN wget https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/${RELEASE_DATE}/documentation/short.fsa && \ | ||
| wget https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/${RELEASE_DATE}/documentation/SubmissionTemplate.sbt && \ | ||
| table2asn -i short.fsa && \ | ||
| table2asn -t SubmissionTemplate.sbt -i short.fsa -o helicase.sqn |
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| # NCBI table2asn | ||
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| Main tool : [table2asn](https://www.ncbi.nlm.nih.gov/genbank/table2asn/) | ||
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| Full documentation: [README](https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/DOCUMENTATION/table2asn_readme.txt) | ||
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| > table2asn is a command-line program that creates sequence records for submission to GenBank | ||
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| There are also a collection of related tools that are included in the image | ||
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| ``` | ||
| agp_validate: 2.29.324 | ||
| asn2all 14.7 | ||
| asn2asn: 1.29.324 | ||
| asn2fasta: 1.29.324 | ||
| asn2flat: 6.29.324 | ||
| asn2fsa 6.1 | ||
| asn2gb 18.7 | ||
| asn2idx 1.1 | ||
| asn2xml 1.0 | ||
| asndisc 2.3 | ||
| asnmacro 1.8 | ||
| asnval 15.7 | ||
| asnvalidate: 3.29.324 | ||
| gap_stats: 4.2.324 (MSS tools matrix (auto-generated)) | ||
| gene2xml 1.6 | ||
| insdseqget 1.1 | ||
| sqn2agp 1.9 | ||
| srcchk: 1.29.324 | ||
| table2asn: 1.29.324 | ||
| ``` | ||
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| ## Example Usage | ||
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| ```bash | ||
| # Single non-genome submission: a particular .fsa file, and only 1 sequence in the .fsa file and the source information is in the definition line of the .fsa file: | ||
| table2asn -t template.sbt -i x.fsa -V v | ||
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| # Batch non-genome submission: a directory that contains .fsa files, and multiple sequences per file, and the source information is in the definition line of the .fsa files: | ||
| table2asn -t template.sbt -indir path_to_files -a s -V v | ||
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| # Genome submission: a directory that contains multiple .fsa files of a single genome, and one or more sequences per file and the source information is in the definition line of the .fsa files: | ||
| table2asn -t template.sbt -indir path_to_files -M n -Z | ||
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| # Genome submission for the most common gapped situation (= runs of 10 or more Ns represent a gap, and there are no gaps of completely unknown size, and the evidence for linkage across the gaps is "paired-ends"), and the source information is in the definition line of the .fsa files: | ||
| table2asn -t template -indir path_to_files -M n -Z -gaps-min 10 -l paired-ends | ||
| ``` | ||
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