diff --git a/README.md b/README.md index 8be978e38..70907b91d 100644 --- a/README.md +++ b/README.md @@ -244,7 +244,7 @@ To learn more about the docker pull rate limits and the open source software pro | [ngmaster](https://hub.docker.com/r/staphb/ngmaster)
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| https://github.com/MDU-PHL/ngmaster | | [NCBI Datasets](https://hub.docker.com/r/staphb/ncbi-datasets)
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| [https://github.com/ncbi/datasets](https://github.com/ncbi/datasets)
[https://www.ncbi.nlm.nih.gov/datasets/docs/v2/](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/) | | [NCBI AMRFinderPlus](https://hub.docker.com/r/staphb/ncbi-amrfinderplus)
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| [https://github.com/ncbi/amr](https://github.com/ncbi/amr) | -| [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
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| [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | +| [NCBI table2asn](https://hub.docker.com/r/staphb/ncbi-table2asn)
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| [https://www.ncbi.nlm.nih.gov/genbank/table2asn/](https://www.ncbi.nlm.nih.gov/genbank/table2asn/)
[https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/](https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/2022-06-14/by_program/table2asn/) | | [ONTime](https://hub.docker.com/r/staphb/ontime)
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| https://github.com/mbhall88/ontime | | [OrthoFinder](https://hub.docker.com/r/staphb/orthofinder)
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| https://github.com/davidemms/OrthoFinder | | [Panaroo](https://hub.docker.com/r/staphb/panaroo)
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Click to see all versions | https://github.com/gtonkinhill/panaroo | diff --git a/build-files/ncbi-table2asn/1.29.324/Dockerfile b/build-files/ncbi-table2asn/1.29.324/Dockerfile new file mode 100644 index 000000000..4c05854cf --- /dev/null +++ b/build-files/ncbi-table2asn/1.29.324/Dockerfile @@ -0,0 +1,78 @@ +ARG RELEASE_DATE="2025-09-16" + +FROM ubuntu:jammy AS app + +# 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 + +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="sage.wright@theiagen.com" + +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 + +WORKDIR /usr/local/bin + +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 " + +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 + +ENV LC_ALL=C + +CMD ["table2asn", "-help"] + +WORKDIR /data + +FROM app AS test + +ARG RELEASE_DATE + +# 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 && ${tool} -version ; done + +WORKDIR /test + +RUN wget https://ftp.ncbi.nlm.nih.gov/asn1-converters/versions/${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 diff --git a/build-files/ncbi-table2asn/1.29.324/README.md b/build-files/ncbi-table2asn/1.29.324/README.md new file mode 100644 index 000000000..03bba3e93 --- /dev/null +++ b/build-files/ncbi-table2asn/1.29.324/README.md @@ -0,0 +1,47 @@ +# NCBI table2asn + +Main tool : [table2asn](https://www.ncbi.nlm.nih.gov/genbank/table2asn/) + +Full documentation: [README](https://ftp.ncbi.nlm.nih.gov/asn1-converters/by_program/table2asn/DOCUMENTATION/table2asn_readme.txt) + +> table2asn is a command-line program that creates sequence records for submission to GenBank + +There are also a collection of related tools that are included in the image + +``` +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 +``` + +## Example Usage + +```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 + +# 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 + +# 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 + +# 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 +```