Index

Symbols

--all nextstrain-logout command line option --allow-remote-access nextstrain-view command line option --ambient nextstrain-build command line option nextstrain-view command line option --attach nextstrain-build command line option --augur nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --auspice nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --aws-batch nextstrain-build command line option --aws-batch-cpus nextstrain-build command line option --aws-batch-job nextstrain-build command line option --aws-batch-memory nextstrain-build command line option --aws-batch-queue nextstrain-build command line option --aws-batch-s3-bucket nextstrain-build command line option --cancel nextstrain-build command line option --conda nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --cpus nextstrain-build command line option --detach nextstrain-build command line option --detach-on-interrupt nextstrain-build command line option --docker nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --docker-arg nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --download nextstrain-build command line option --dry-run nextstrain-deploy command line option nextstrain-remote-delete command line option nextstrain-remote-download command line option nextstrain-remote-upload command line option nextstrain-setup command line option --env nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --envdir nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --exclude-from-download nextstrain-build command line option --exclude-from-upload nextstrain-build command line option --exec nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --fauna nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --force nextstrain-setup command line option --help nextstrain command line option nextstrain-authorization command line option nextstrain-build command line option nextstrain-check-setup command line option nextstrain-debugger command line option nextstrain-deploy command line option nextstrain-init-shell command line option nextstrain-login command line option nextstrain-logout command line option nextstrain-remote command line option nextstrain-remote-delete command line option nextstrain-remote-download command line option nextstrain-remote-list command line option nextstrain-remote-upload command line option nextstrain-setup command line option nextstrain-shell command line option nextstrain-update command line option nextstrain-version command line option nextstrain-view command line option nextstrain-whoami command line option

--help-all nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --host nextstrain-view command line option --image nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --memory nextstrain-build command line option --no-download nextstrain-build command line option --no-logs nextstrain-build command line option --no-open nextstrain-view command line option --no-prompt nextstrain-login command line option --open nextstrain-view command line option --port nextstrain-view command line option --recursively nextstrain-remote-delete command line option nextstrain-remote-download command line option --renew nextstrain-login command line option --sacra nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --set-default nextstrain-check-setup command line option nextstrain-setup command line option --singularity nextstrain-build command line option nextstrain-shell command line option nextstrain-view command line option --username nextstrain-login command line option --verbose nextstrain-version command line option -h nextstrain command line option nextstrain-authorization command line option nextstrain-build command line option nextstrain-check-setup command line option nextstrain-debugger command line option nextstrain-deploy command line option nextstrain-init-shell command line option nextstrain-login command line option nextstrain-logout command line option nextstrain-remote command line option nextstrain-remote-delete command line option nextstrain-remote-download command line option nextstrain-remote-list command line option nextstrain-remote-upload command line option nextstrain-setup command line option nextstrain-shell command line option nextstrain-update command line option nextstrain-version command line option nextstrain-view command line option nextstrain-whoami command line option -r nextstrain-remote-delete command line option nextstrain-remote-download command line option -u nextstrain-login command line option ... nextstrain-build command line option nextstrain-shell command line option <directory> nextstrain-build command line option nextstrain-shell command line option <file> nextstrain-deploy command line option nextstrain-remote-upload command line option <local-path> nextstrain-remote-download command line option <path> nextstrain-view command line option <remote-url> nextstrain-authorization command line option nextstrain-deploy command line option nextstrain-login command line option nextstrain-logout command line option nextstrain-remote-delete command line option nextstrain-remote-download command line option nextstrain-remote-list command line option nextstrain-remote-upload command line option nextstrain-whoami command line option <runtime> nextstrain-check-setup command line option nextstrain-setup command line option nextstrain-update command line option

A

authorization nextstrain command line option aws-batch.cpus

aws-batch.job aws-batch.memory aws-batch.queue aws-batch.s3-bucket

B

build nextstrain command line option

C

check-setup nextstrain command line option computing environment computing platform configuration variable aws-batch.cpus aws-batch.job aws-batch.memory aws-batch.queue aws-batch.s3-bucket core.runner docker.image singularity.image

core.runner

D

debugger nextstrain command line option delete nextstrain-remote command line option

deploy nextstrain command line option docker.image download nextstrain-remote command line option

E

environment variable AWS_ACCESS_KEY_ID AWS_SECRET_ACCESS_KEY HOST, [1] NEXTSTRAIN_AWS_BATCH_CPUS NEXTSTRAIN_AWS_BATCH_JOB NEXTSTRAIN_AWS_BATCH_MEMORY NEXTSTRAIN_AWS_BATCH_QUEUE NEXTSTRAIN_AWS_BATCH_S3_BUCKET NEXTSTRAIN_CONDA_BASE_PACKAGE NEXTSTRAIN_CONDA_CHANNEL NEXTSTRAIN_CONDA_MICROMAMBA_VERSION NEXTSTRAIN_CONFIG, [1] NEXTSTRAIN_DISABLE_NARRATIVE_IMAGE_EMBEDDING NEXTSTRAIN_DOCKER_IMAGE NEXTSTRAIN_DOT_ORG NEXTSTRAIN_HOME, [1] NEXTSTRAIN_LOCK NEXTSTRAIN_PASSWORD NEXTSTRAIN_RUNTIMES NEXTSTRAIN_SECRETS NEXTSTRAIN_SHELL_HISTORY NEXTSTRAIN_SINGULARITY_IMAGE NEXTSTRAIN_USERNAME, [1] PORT, [1]

H

HOST

I

init-shell nextstrain command line option

L

list nextstrain-remote command line option login nextstrain command line option

logout nextstrain command line option

N

nextstrain command line option --help -h authorization build check-setup debugger deploy init-shell login logout remote setup shell update version view whoami nextstrain-authorization command line option --help -h <remote-url> nextstrain-build command line option --ambient --attach --augur --auspice --aws-batch --aws-batch-cpus --aws-batch-job --aws-batch-memory --aws-batch-queue --aws-batch-s3-bucket --cancel --conda --cpus --detach --detach-on-interrupt --docker --docker-arg --download --env --envdir --exclude-from-download --exclude-from-upload --exec --fauna --help --help-all --image --memory --no-download --no-logs --sacra --singularity -h ... <directory> nextstrain-check-setup command line option --help --set-default -h <runtime> nextstrain-debugger command line option --help -h nextstrain-deploy command line option --dry-run --help -h <file> <remote-url> nextstrain-init-shell command line option --help -h shell nextstrain-login command line option --help --no-prompt --renew --username -h -u <remote-url> nextstrain-logout command line option --all --help -h <remote-url> nextstrain-remote command line option --help -h delete download list upload

nextstrain-remote-delete command line option --dry-run --help --recursively -h -r <remote-url> nextstrain-remote-download command line option --dry-run --help --recursively -h -r <local-path> <remote-url> nextstrain-remote-list command line option --help -h <remote-url> nextstrain-remote-upload command line option --dry-run --help -h <file> <remote-url> nextstrain-setup command line option --dry-run --force --help --set-default -h <runtime> nextstrain-shell command line option --augur --auspice --conda --docker --docker-arg --env --envdir --exec --fauna --help --help-all --image --sacra --singularity -h ... <directory> nextstrain-update command line option --help -h <runtime> nextstrain-version command line option --help --verbose -h nextstrain-view command line option --allow-remote-access --ambient --augur --auspice --conda --docker --docker-arg --env --envdir --exec --fauna --help --help-all --host --image --no-open --open --port --sacra --singularity -h <path> nextstrain-whoami command line option --help -h <remote-url> NEXTSTRAIN_CONFIG NEXTSTRAIN_HOME NEXTSTRAIN_USERNAME

P

PORT

R

remote nextstrain command line option

runner runtime

S

setup nextstrain command line option shell nextstrain command line option nextstrain-init-shell command line option

singularity.image

U

update nextstrain command line option

upload nextstrain-remote command line option

V

version nextstrain command line option

view nextstrain command line option

W

whoami nextstrain command line option