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Merge pull request #1568 from cwoodside1278/seqsender-1.3.91
Update Seqsender to 1.3.93 version
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‎README.md‎

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| [Samtools](https://hub.docker.com/r/staphb/samtools) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/samtools)](https://hub.docker.com/r/staphb/samtools) | <details><summary>Click to see all versions</summary> <ul><li>[1.9](./build-files/samtools/1.9/)</li><li>[1.10](./build-files/samtools/1.10/)</li><li>[1.11](./build-files/samtools/1.11/)</li><li>[1.12](./build-files/samtools/1.12/)</li><li>[1.13](./build-files/samtools/1.13/)</li><li>[1.14](./build-files/samtools/1.14/)</li><li>[1.15](./build-files/samtools/1.15/)</li><li>[1.16](./build-files/samtools/1.16/)</li><li>[1.16.1](./build-files/samtools/1.16.1/)</li><li>[1.17](./build-files/samtools/1.17/)</li><li>[1.17-2023-06](./build-files/samtools/1.17-2023-06/)</li><li>[1.18](./build-files/samtools/1.18/)</li><li>[1.19](./build-files/samtools/1.19/)</li><li>[1.20](./build-files/samtools/1.20/)</li><li>[1.20.c](./build-files/samtools/1.20.c/)</li><li>[1.21](./build-files/samtools/1.21/)</li><li>[1.22](./build-files/samtools/1.22/)</li><li>[1.22.1](./build-files/samtools/1.22.1/)</li><li>[1.23](./build-files/samtools/1.23/)</li></ul> </details> | https://github.com/samtools/samtools |
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| [SeqFu](https://hub.docker.com/r/staphb/SeqFu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqfu)](https://hub.docker.com/r/staphb/seqfu) | <details><summary>Click to see all versions</summary> <ul><li>[1.20.3](./build-files/seqfu/1.20.3/)</li><li>[1.22.3](./build-files/seqfu/1.22.3/)</li><li>[1.23.0](./build-files/seqfu/1.23.0/)</li></ul> </details> | https://github.com/telatin/seqfu2 |
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| [SeqKit](https://hub.docker.com/r/staphb/SeqKit) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqkit)](https://hub.docker.com/r/staphb/seqkit) | <details><summary>Click to see all versions</summary> <ul><li>[2.3.1](./build-files/seqkit/2.3.1/)</li><li>[2.6.1](./build-files/seqkit/2.6.1/)</li><li>[2.7.0](./build-files/seqkit/2.7.0/)</li><li>[2.8.0](./build-files/seqkit/2.8.0/)</li><li>[2.8.1](./build-files/seqkit/2.8.1/)</li><li>[2.8.2](./build-files/seqkit/2.8.2/)</li><li>[2.9.0](./build-files/seqkit/2.9.0/)</li><li>[2.10.0](./build-files/seqkit/2.10.0/)</li><li>[2.10.1](./build-files/seqkit/2.10.1/)</li><li>[2.12.0](./build-files/seqkit/2.12.0/)</li></ul> </details> | https://github.com/shenwei356/seqkit |
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| [SeqSender](https://hub.docker.com/r/staphb/seqsender/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsender)](https://hub.docker.com/r/staphb/seqsender) | <details><summary>Click to see all versions</summary> <ul><li>[1.3.3](./build-files/seqsender/1.3.3/)</li><li>[1.3.4](./build-files/seqsender/1.3.4/)</li><li>[1.3.6](./build-files/seqsender/1.3.6/)</li><li>[1.3.9](./build-files/seqsender/1.3.9/)</li></ul> </details> | https://github.com/CDCgov/seqsender |
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| [SeqSender](https://hub.docker.com/r/staphb/seqsender/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsender)](https://hub.docker.com/r/staphb/seqsender) | <details><summary>Click to see all versions</summary> <ul><li>[1.3.3](./build-files/seqsender/1.3.3/)</li><li>[1.3.4](./build-files/seqsender/1.3.4/)</li><li>[1.3.6](./build-files/seqsender/1.3.6/)</li><li>[1.3.9](./build-files/seqsender/1.3.9/)</li><li>[1.3.93](./build-files/seqsender/1.3.93/)</li></ul> </details> | https://github.com/CDCgov/seqsender |
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| [SeqSero](https://hub.docker.com/r/staphb/seqsero/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero)](https://hub.docker.com/r/staphb/seqsero) | <details><summary>Click to see all versions</summary> <ul><li>[1.0.1](./build-files/seqsero/1.0.1/)</li></ul> </details> | https://github.com/denglab/SeqSero |
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| [SeqSero2](https://hub.docker.com/r/staphb/seqsero2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero2)](https://hub.docker.com/r/staphb/seqsero2) | <details><summary>Click to see all versions</summary> <ul><li>[0.1.0](./build-files/seqsero2/0.1.0/)</li><li>[1.0.0](./build-files/seqsero2/1.0.0/)</li><li>[1.0.2](./build-files/seqsero2/1.0.2/)</li><li>[1.1.0](./build-files/seqsero2/1.1.0/)</li><li>[1.1.1](./build-files/seqsero2/1.1.1/)</li><li>[1.2.1](./build-files/seqsero2/1.2.1/)</li><li>[1.3.1](./build-files/seqsero2/1.3.1/)</li><li>[1.3.1-micromamba](./build-files/seqsero2/1.3.1-micromamba/)</li><li>[1.3.2](./build-files/seqsero2/1.3.2/)</li></ul> </details> | https://github.com/denglab/SeqSero2/ |
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| [SeqSero2S](https://hub.docker.com/r/staphb/seqsero2s/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/seqsero2s)](https://hub.docker.com/r/staphb/seqsero2s) | <details><summary>Click to see all versions</summary> <ul><li>[1.1.4](./build-files/seqsero2s/1.1.4/)</li> </details> | https://github.com/LSTUGA/SeqSero2S/ |

‎build-files/seqsender/1.3.93/Dockerfile‎

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# sourced from https://github.com/StaPH-B/docker-builds/blob/master/dockerfile-template/Dockerfile_mamba
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FROM mambaorg/micromamba:2.5.0-ubuntu24.04 AS app
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ARG SEQSENDER_VERSION=1.3.93
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# build and run as root users since micromamba image has 'mambauser' set as the $USER
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USER root
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# set workdir to default for building; set to /data at the end
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WORKDIR /
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LABEL base.image="mambaorg/micromamba:2.5.0-ubuntu24.04"
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LABEL dockerfile.version="1"
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LABEL software="SeqSender"
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LABEL software.version="${SEQSENDER_VERSION}"
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LABEL description="Python program that automates the process of generating submission files and batch uploading to NCBI archives and GISAID databases"
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LABEL website="https://github.com/CDCgov/seqsender"
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LABEL license="https://github.com/CDCgov/seqsender/blob/master/LICENSE"
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LABEL maintainer="Vincent Tu"
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LABEL maintainer.email="vincent.tu@phila.gov"
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# install dependencies and cleanup apt garbage
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RUN apt-get update && apt-get install -y --no-install-recommends \
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wget \
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ca-certificates \
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procps \
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libsqlite3-0 && \
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apt-get autoclean && rm -rf /var/lib/apt/lists/*
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# download source code; make /data
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RUN wget -q https://github.com/CDCgov/seqsender/archive/refs/tags/v${SEQSENDER_VERSION}.tar.gz && \
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tar -xzf v${SEQSENDER_VERSION}.tar.gz && \
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rm -r v${SEQSENDER_VERSION}.tar.gz && \
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mkdir /data
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# set PATH and locale settings for singularity
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ENV LC_ALL=C.UTF-8 \
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PATH=/opt/conda/bin/:${PATH}:/seqsender-${SEQSENDER_VERSION}
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# increase number of open files
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# install software into the base micromamba environment, pinning the version
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# clean up conda garbage
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RUN micromamba install --yes --name base -f "/seqsender-${SEQSENDER_VERSION}/env.yaml" && \
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micromamba clean --all --force-pkgs-dirs --yes
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# default command is to pull up help options
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CMD ["seqsender.py", "--help"]
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# set working directory to /data
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WORKDIR /data
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# test layer
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FROM app AS test
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# print version and grep for it; if not found, exit with error
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RUN seqsender.py --help && \
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seqsender.py version | \
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grep "Version: ${SEQSENDER_VERSION}" || exit 1
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# generate test data for FLU and COV and check if directories are created; otherwise exit with error
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RUN for org in FLU COV; \
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do seqsender.py test_data -bsng --organism "${org}" --submission_dir test_dir && \
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test -d "test_dir/${org}_TEST_DATA/" || exit 1; \
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done
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# test network connection
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RUN seqsender.py test_network_connection | \
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grep "No network connection issues detected" || exit 1
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RUN micromamba list -n base

‎build-files/seqsender/1.3.93/README.md‎

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# SeqSender 1.3.93 container
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Main tool: [SeqSender](https://github.com/CDCgov/seqsender)
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<details>
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<summary>Additional tools installed via micromamba:</summary>
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```
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List of packages in environment: "/opt/conda"
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Name Version Build Channel
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──────────────────────────────────────────────────────────────────────
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Cerberus 1.3.5 pypi_0 pypi
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_libgcc_mutex 0.1 conda_forge conda-forge
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_openmp_mutex 4.5 2_gnu conda-forge
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annotated-types 0.6.0 pyhd8ed1ab_0 conda-forge
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biopython 1.83 py38h01eb140_0 conda-forge
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brotli-python 1.1.0 py38h17151c0_1 conda-forge
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bzip2 1.0.8 hd590300_5 conda-forge
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ca-certificates 2024.2.2 hbcca054_0 conda-forge
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certifi 2024.2.2 pyhd8ed1ab_0 conda-forge
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charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
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icu 73.2 h59595ed_0 conda-forge
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idna 3.6 pyhd8ed1ab_0 conda-forge
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importlib-metadata 7.1.0 pyha770c72_0 conda-forge
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importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
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ld_impl_linux-64 2.40 h41732ed_0 conda-forge
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libblas 3.9.0 21_linux64_openblas conda-forge
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libcblas 3.9.0 21_linux64_openblas conda-forge
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libffi 3.4.2 h7f98852_5 conda-forge
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libgcc-ng 13.2.0 h807b86a_5 conda-forge
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libgfortran-ng 13.2.0 h69a702a_5 conda-forge
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libgfortran5 13.2.0 ha4646dd_5 conda-forge
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libgomp 13.2.0 h807b86a_5 conda-forge
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libiconv 1.17 hd590300_2 conda-forge
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liblapack 3.9.0 21_linux64_openblas conda-forge
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libnsl 2.0.1 hd590300_0 conda-forge
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libopenblas 0.3.26 pthreads_h413a1c8_0 conda-forge
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libsqlite 3.45.2 h2797004_0 conda-forge
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libstdcxx-ng 13.2.0 h7e041cc_5 conda-forge
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libuuid 2.38.1 h0b41bf4_0 conda-forge
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libxcrypt 4.4.36 hd590300_1 conda-forge
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libxml2 2.12.6 h232c23b_1 conda-forge
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libxslt 1.1.39 h76b75d6_0 conda-forge
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libzlib 1.2.13 hd590300_5 conda-forge
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lxml 5.1.0 py38h32ae189_0 conda-forge
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multimethod 1.9.1 pyhd8ed1ab_0 conda-forge
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mypy_extensions 1.0.0 pyha770c72_0 conda-forge
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nameparser 1.1.3 pypi_0 pypi
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ncurses 6.4.20240210 h59595ed_0 conda-forge
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numpy 1.24.4 py38h59b608b_0 conda-forge
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openssl 3.2.1 hd590300_1 conda-forge
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packaging 24.0 pyhd8ed1ab_0 conda-forge
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pandas 2.0.3 py38h01efb38_1 conda-forge
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pandera 0.18.3 hd8ed1ab_0 conda-forge
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pandera-base 0.18.3 pyhd8ed1ab_0 conda-forge
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pip 24.0 pyhd8ed1ab_0 conda-forge
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pydantic 2.6.4 pyhd8ed1ab_0 conda-forge
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pydantic-core 2.16.3 py38h0cc4f7c_0 conda-forge
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pysocks 1.7.1 pyha2e5f31_6 conda-forge
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python 3.8.19 hd12c33a_0_cpython conda-forge
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python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
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python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
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python_abi 3.8 4_cp38 conda-forge
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pytz 2024.1 pyhd8ed1ab_0 conda-forge
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pyyaml 6.0.1 py38h01eb140_1 conda-forge
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readline 8.2 h8228510_1 conda-forge
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requests 2.31.0 pyhd8ed1ab_0 conda-forge
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setuptools 69.2.0 pyhd8ed1ab_0 conda-forge
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six 1.16.0 pyh6c4a22f_0 conda-forge
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tk 8.6.13 noxft_h4845f30_101 conda-forge
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typeguard 4.2.1 pyhd8ed1ab_0 conda-forge
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typing-extensions 4.10.0 hd8ed1ab_0 conda-forge
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typing_extensions 4.10.0 pyha770c72_0 conda-forge
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typing_inspect 0.9.0 pyhd8ed1ab_0 conda-forge
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urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
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wheel 0.43.0 pyhd8ed1ab_1 conda-forge
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wrapt 1.16.0 py38h01eb140_0 conda-forge
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xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge
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xz 5.2.6 h166bdaf_0 conda-forge
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yaml 0.2.5 h7f98852_2 conda-forge
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zipp 3.17.0 pyhd8ed1ab_0 conda-forge
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```
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</details>
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Documentation: [https://cdcgov.github.io/seqsender](https://cdcgov.github.io/seqsender)
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SeqSender is a public database submission pipeline by the CDC.
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## Example Usage
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```bash
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# Create test submission files with supplied Influenza data
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docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data seqsender:1.3.3 seqsender.py test_data -bsng --organism FLU --submission_dir test_dir
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# Create test submission files with supplied SARS-CoV-2 data
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docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data seqsender:1.3.3 seqsender.py test_data -bsng --organism COV --submission_dir test_dir
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```
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View full `seqsender` help options: `docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data seqsender:1.3.3 seqsender.py --help`

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