delete (clean)
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Delete DRS objects and the associated files in cloud storage by DRS ID, DRS name, or DRS tag. |
id
Specify the IDs of the DRS objects that you want to delete (optional).
names str [str ...]
Specify the names of the DRS objects that you want to delete (optional).
tags str [str ...]
Specify the labels of the DRS objects that you want to delete (optional).
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download
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Download the content of a DRS object to a file or directory path. |
workspace STR
Specify the workspace based on the signed in account (required).
dst STR
Show the destination directory or file path.
id STR
A DRS object ID (required if there is no self URI).
uri URI
A DRS self URI (required if there is no DRS ID).
overwrite
Overwrite the existing files (optional, default = false).
output {json,table,tsv}
Specify the output format of the stdout file (optional, default = json).
chunk-size {4,8,16,32}
Specify the size of chunk in the chunked downloading
process. If the specified size is greater than 4MiB, the md5
hashes are not checked. (optional, default = 4MiB).
concurrency
Specify the transmission concurrency in file uploading. The upload bandwidth can be modified using the formula concurrency * chunk-size * multiprocessing (default = 64).
multiprocessing
Specify the number of files that you want to upload at any given time. (optional, default = 1).
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get (retrieve)
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Get a DRS object. |
workspace STR
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register-blob
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Register a DRS object as a blob. |
workspace STR
Specify the workspace based on the signed in account (required).
type STR
To register a file as a blob, use file. To register a folder as a blob, use folder (required).
name
Specify the name of the object that you want to register (optional in stdin mode, otherwise required).
file-type
Specify the file type of the object that you want to register (optional in stdin mode, otherwise required). For example, application/json.
mime-type
Specify the MIME type of the object that you want to register (optional stdin mode, otherwise required). For example, application/json.
description
Specify the description of the object that you want to register (optional).
aliases
Specify the aliases of the object that you want to register (optional).
output {json,table,tsv}
Specify the output format of the stdout file (optional, default = json).
stdin
Specify whether or not you want to enable stdin mode (optional). Selecting stdin prevents you from enabling any of the other options and the JSON object must therefore contain all the required keys [name, file-type, mime-type,
description, aliases, tags, created-time, updated-time, size, urls, access-tiers, regions, Authorizations, checksum, checksum-type, metadata].
id STR
Specify a custom DRS object ID (optional).
metadata STR
Specify a JSON string describing the metadata of the object you want to register (optional).
checksum-type {sha256}
Specify the type of checksum (optional in stdin mode, otherwise required). At the moment, only sha256 is supported.
checksum STR
Specify the checksum of the object that you want to register. The checksum type must be sha256. If the DRS type is blob, this argument is required (optional in stdin mode, otherwise required).
size INT
Specify the size of the object that you want to register. If the DRS type is blob, this argument is required (optional in stdin mode, otherwise required).
access-methods
Specify the access methods of the object that you want to register.
updated-time STR
Provide the timestamp of when an object was updated. The time format must be in RFC3339. If the DRS type is blob,
this argument is required (optional in stdin mode). For example, 2021-09-13 02:54:03.636044+00:00.
created-time STR
Provide the timestamp of when an object was first created in the storage location. The time format must be in RFC3339. If the DRS type is blob, this argument is required (optional in stdin mode). For example, 2021-09-13 02:54:03.636044+00:00.
tags str [str ...]
Specify the tags that you want to use for the object that you want to register (optional).
deleted-time STR
Specify a date in the format YYYY-MM-DD to set the automatic deletion time for the DRS object, e.g. 2024-01-01 (optional).
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register-bundle
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Register a DRS object as a bundle. |
name STR
Specify the name of the object that you want to register (must not be in stdin mode, otherwise required).
workspace STR
Specify the workspace based on the signed in account (required).
drs-id STR
Specify the DRS object ID that will be registered in the bundle (required).
output {json,table,tsv}
Specify the output format of the stdout file (optional, default = json).
id STR
Specify a custom DRS bundle ID (optional).
metadata STR
Specify a JSON string describing the metadata of the bundle you want to register (optional).
tags str [str ...]
Specify the tags that you want to use for the bundle that you want to register (optional).
aliases str [str ...]
Specify the aliases of the bundle that you want to register (optional).
description STR
Specify the description of the bundle that you want to register (optional).
deleted-time STR
Specify a date in the format YYYY-MM-DD to set the automatic deletion time for the DRS object, e.g. 2024-01-01 (optional).
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search
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Locate DRS objects either by name or by tag. Do not combine names and labels in a single query. |
tags str [str ...]
Locate a DRS object using a list of labels (optional).
names str [str ...]
Locate a DRS object using a list of names (optional).
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update (patch)
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Update a DRS object |
workspace STR
Specify the workspace based on the signed in account (required).
id STR
Specify the DRS object ID (required).
stdin
Provide a DRS object payload using the stdin mode (optional). Selecting stdin prevents you from enabling any of the other options and the JSON object must therefore contain all the required keys [name, tags, metadata, checksum, checksum-type, updated-time].
updated-time STR
Specify the timestamp when the DRS object was updated (optional). The time format must be in RFC3339. For example, 2021-09-13 02:54:03.636044+00:00.
checksum-type {sha256}
Specify the DRS object checksum type (required when checksum is given).
checksum STR
Specify the DRS object checksum (required when
checksum-type is given).
metadata METADATA
Specify the DRS object metadata (optional).
tags str [str ...]
Specify the DRS object tags (optional).
name STR
Specify the DRS object name (optional).
deleted-time STR
Specify a date in the format YYYY-MM-DD to set the automatic deletion time for the DRS object, e.g. 2024-01-01 (optional).
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upload (copy)
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Upload data from the local file system to a SeqsLab Data Hub cloud service. Upload command behaves similarly to gsutil cp command.
Besides, |
workspace STR
Specify the workspace based on the signed in account (required).
src SRC
Specify the source directory, file path, or DRS URL (required).
dst DST
Specify the destination directory, file path, or DRS URL. Paths with leading slashes, leading backslashes, or dot-only segments are invalid. Additionally, paths should not contain characters other than [0-9a-zA-Z-._:/]. If not provided, the default is the current Linux epoch timestamp (optional).
recursive (-r)
Copy an entire directory tree (optional, default = False).
output {json,table,tsv}
Specify the stdout format (default = json).
concurrency INT
Specify the transmission concurrency in file uploading. The
upload bandwidth can be modified using the formula
concurrency * chunk-size * multiprocessing (default = 64).
multiprocessing INT
Specify the number of files that you want to upload at any given time. (default = 1).
chunk-size {8,16}
Specify the size of each file that you want to upload in mebibytes (MiB). (default = 8MiB).
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upload-runsheet (runsheet)
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Upload samples based on the Run Sheet and FASTQ path information. |
workspace STR
Specify the workspace based on the signed in account (required).
input-dir STR
Specify the FASTQ file path (required).
run-sheet STR
Specify the Run Sheet file path (required).
upload-dst STR
Specify the upload destination path (optional).
fastq_signature STR
Define a fastq path matching pattern using ~{} wrapping syntax for Runsheet column names. For example, ~{Sample_Name}_S~{Sample_ID} matches NA12878_S1.fastq.gz with Sample_Name as NA12878 and Sample_ID as 1 (optional, defaulting to ~{Sample_ID}).
concurrency INT
Specify the transmission concurrency in file uploading. The
upload bandwidth can be modified using the formula
concurrency * chunk-size * multiprocessing (default = 64).
multiprocessing INT
Specify the number of files that you want to upload at any given time. (default = 1).
chunk-size {8,16}
Specify the size of each file that you want to upload in mebibyte (MiB). (default = 8MiB).
seq-run-id
Specify a runsheet header field as a sequencer run identifier; the specified value will be used as a sequencer run specific label for future dataset management (optional).
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share
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Generate a share link enabling external users to download the DRS object as a zip archive through web browsers.
The share link expires either after the first successful download or after a period of three months. |
id str
Specify the ID of the DRS object that you want to share (required).
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add-reads-runsheet (add-reads)
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Identify and patch existing DRS object with add-reads runsheet label for runsheet-based run triggering for DRS
auto-matching. |
workspace STR
Specify the workspace based on the signed in account (required).
run-sheet STR
Specify the Run Sheet file path (required).
seq-run-id
Specify a runsheet header field as a sequencer run identifier; the specified value will be used as a sequencer run specific label for future dataset management (optional).
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