### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Info File Example - ENA Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli Example of a separate info file used for backward compatibility in ENA submissions. This file contains metadata fields and must be referenced in the main manifest file using the `INFO` field. ```text INFO assembly.info FASTA genome.fasta.gz ``` -------------------------------- ### Untitled No description -------------------------------- ### Example Manifest File (Webin-CLI) Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/sequence Demonstrates the structure of a manifest file for Webin-CLI submissions. It requires STUDY and NAME fields, and optionally supports DESCRIPTION, FLATFILE, or TAB fields. FLATFILE and TAB are mutually exclusive. ```text STUDY todo NAME todo FLATFILE .embl.gz ``` ```text STUDY todo NAME todo TAB .tsv.gz ``` -------------------------------- ### Run Webin-CLI Java Jar Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli This snippet demonstrates how to execute the Webin-CLI program as a self-executing Java JAR file. It requires Java to be installed and specifies the JAR file path along with any necessary command-line options. The example shows variations for Mac/Linux and Windows operating systems. ```bash java -jar webin-cli-.jar java -jar webin-cli-1.7.3.jar # Example for Mac/Linux: java -jar Downloads/webin-cli-1.7.3.jar # Example for Windows: java -jar Downloads\webin-cli-1.7.3.jar ``` -------------------------------- ### Text Manifest File Example - ENA Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli Example of a text-based manifest file used for ENA submissions. This format uses tab-separated values to define metadata fields and file names. It's suitable for simpler submissions. ```text STUDY Study accession or unique name (alias) SAMPLE Sample accession or unique name (alias) ANALYSIS_REF Comma separated list of analysis accession(s) RUN_REF Comma separated list of run accession(s) FASTA genome.fasta.gz STUDY TODO SAMPLE TODO ASSEMBLYNAME TODO COVERAGE TODO PROGRAM TODO PLATFORM TODO MINGAPLENGTH TODO MOLECULETYPE genomic DNA FASTA genome.fasta.gz ``` -------------------------------- ### Example Manifest File for Webin-CLI (Flatfile) Source: https://ena-docs.readthedocs.io/en/latest/submit/sequence This example demonstrates the structure of a manifest file for sequence submission using a flat file. It includes mandatory fields STUDY and NAME, and the FLATFILE field pointing to the sequence data file. ```text STUDY todo NAME todo FLATFILE .embl.gz ``` -------------------------------- ### Untitled No description -------------------------------- ### Using Aspera for Webin-CLI File Uploads Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli Specifying the use of the Aspera protocol for file uploads with Webin-CLI via the -ascp option. Requires Aspera CLI to be installed and its directory included in the system's PATH. ```shell webin-cli-.jar -ascp ``` -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Manifest File Example for Binned Metagenome Assembly Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/assembly/metagenome/binned An example of a manifest file used for binned metagenome assembly submissions. It specifies required metadata fields and the location of the FASTA file containing the sequences. Fields are tab-separated. ```text STUDY TODO SAMPLE TODO RUN_REF TODO ASSEMBLYNAME TODO ASSEMBLY_TYPE TODO COVERAGE TODO PROGRAM TODO PLATFORM TODO MINGAPLENGTH TODO MOLECULETYPE genomic DNA FASTA binned_metagenome.fasta.gz ``` -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Webin-CLI Advanced Submission Options Source: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli These options provide advanced control over the Webin-CLI submission process, such as using a test service, enabling Aspera CLI for faster transfers, and retrieving program version or help information. These are useful for testing and optimizing submissions. ```bash # Advanced options: -test -ascp -version -help ``` -------------------------------- ### Sequence Record FASTA Example Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/analyses/taxonomic-reference-set Example format for sequence records within a multi-FASTA file for Taxonomic Reference Sets. Each record starts with an ID line, which must uniquely identify the sequence and match an identifier in the sequence metadata table. Additional details can be appended after a '|'. ```fasta >ITS1DB00588027|162468|Steinernema abbasi|ITS1 located by ENA annotation, 267bp ATCGactgRYSWKMBDHVryswkmbdhvNn ``` -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Webin-CLI Submission Command Example Source: https://ena-docs.readthedocs.io/en/latest/submit/analyses/taxonomic-reference-set An example command for using the Webin-CLI tool to validate or submit sequence metadata. This command requires username, password, context, and manifest file path. It includes options for validation or submission, and an optional test server flag. ```bash webin-cli -username Webin-99999 -password xxxxxx -context taxrefset -manifest trs_submission.txt -validate ``` -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Example BioProject Accession XML - ENA Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/study/programmatic This XML snippet demonstrates how a BioProject accession number, typically starting with 'PRJEB', is presented in the ENA submission receipt. It includes attributes like accession, alias, and status. ```xml ``` -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Untitled No description -------------------------------- ### Example Submission XML for Adding Objects Source: https://ena-docs.readthedocs.io/en/latest/_sources/submit/analyses/sequence-annotation This is a basic Submission XML file used to instruct ENA on actions to take. The example shows the `` action, indicating that new objects should be submitted. ```xml ``` -------------------------------- ### Untitled No description -------------------------------- ### Show Help for enaDataGet Command Source: https://ena-docs.readthedocs.io/en/latest/_sources/retrieval/programmatic-access/browser-tools Displays the available arguments and usage instructions for the `enaDataGet` command. This is useful for understanding the command's capabilities and options before downloading data. No specific inputs are required other than the command itself. ```bash > enaDataGet --help ``` -------------------------------- ### Untitled No description