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