| Name | assembly-uploader JSON |
| Version |
1.0.1
JSON |
| download |
| home_page | None |
| Summary | Python scripts to upload primary metagenome and metatranscriptome assemblies to ENA on a per-study basis. This script generates xmls to register a new study and create manifests necessary for submission with webin-cli. |
| upload_time | 2024-06-10 16:13:35 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | Apache Software License 2.0 |
| keywords |
bioinformatics
tool
metagenomics
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Public ENA Assembly uploader
Upload of metagenome and metatranscriptome assemblies to the [European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena)
Pre-requisites:
- CSV metadata file. One per study. See test/fixtures/test_metadata for an example
- Compressed assembly fasta files in the locations defined in the metadata file
Set the following environmental variables with your webin details:
ENA_WEBIN
```
export ENA_WEBIN=Webin-0000
```
ENA_WEBIN_PASSWORD
```
export ENA_WEBIN_PASSWORD=password
```
## Installation
Install the package:
```bash
pip install assembly_uploader
```
## Register study and generate pre-upload files
**If you already have a registered study accession for your assembly files skip to step 3.**
### Step 1
This step will generate a folder STUDY_upload and a project XML and submission XML within it:
```bash
study_xmls
--study STUDY raw reads study ID
--library LIBRARY metagenome or metatranscriptome
--center CENTER center for upload e.g. EMG
--hold HOLD hold date (private) if it should be different from the provided study in format dd-mm-yyyy. Will inherit the release date of the raw read study if not
provided.
--tpa is the study a third party assembly. Default True
--publication PUBLICATION
pubmed ID for connected publication if available
```
### Step 2
This step submit the XML to ENA and generate a new assembly study accession. Keep note of the newly generated study accession:
```bash
submit_study
--study STUDY raw reads study ID
--test run test submission only
```
### Step 3
This step will generate manifest files in the folder STUDY_UPLOAD for runs specified in the metadata file:
```bash
assembly_manifest
--study STUDY raw reads study ID
--data DATA metadata CSV - run_id, coverage, assembler, version, filepath
--assembly_study ASSEMBLY_STUDY
pre-existing study ID to submit to if available. Must exist in the webin account
--force overwrite all existing manifests
```
## Upload assemblies
Once manifest files are generated, it is necessary to use ENA's webin-cli resource to upload genomes.
To test your submission add the `-test` argument.
A live execution example within this repo is the following:
```bash
ena-webin-cli \
-context=genome \
-manifest=SRR12240187.manifest \
-userName=$ENA_WEBIN \
-password=$ENA_WEBIN_PASSWORD \
-submit
```
More information on ENA's webin-cli can be found [here](<https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html>).
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"description": "# Public ENA Assembly uploader\nUpload of metagenome and metatranscriptome assemblies to the [European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena)\n\nPre-requisites:\n- CSV metadata file. One per study. See test/fixtures/test_metadata for an example\n- Compressed assembly fasta files in the locations defined in the metadata file\n\nSet the following environmental variables with your webin details:\n\nENA_WEBIN\n```\nexport ENA_WEBIN=Webin-0000\n```\n\nENA_WEBIN_PASSWORD\n```\nexport ENA_WEBIN_PASSWORD=password\n```\n\n## Installation\n\nInstall the package:\n\n```bash\npip install assembly_uploader\n```\n\n## Register study and generate pre-upload files\n\n**If you already have a registered study accession for your assembly files skip to step 3.**\n\n### Step 1\n\nThis step will generate a folder STUDY_upload and a project XML and submission XML within it:\n\n```bash\nstudy_xmls\n --study STUDY raw reads study ID\n --library LIBRARY metagenome or metatranscriptome\n --center CENTER center for upload e.g. EMG\n --hold HOLD hold date (private) if it should be different from the provided study in format dd-mm-yyyy. Will inherit the release date of the raw read study if not\n provided.\n --tpa is the study a third party assembly. Default True\n --publication PUBLICATION\n pubmed ID for connected publication if available\n```\n\n### Step 2\n\nThis step submit the XML to ENA and generate a new assembly study accession. Keep note of the newly generated study accession:\n\n```bash\nsubmit_study\n --study STUDY raw reads study ID\n --test run test submission only\n```\n\n\n### Step 3\n\nThis step will generate manifest files in the folder STUDY_UPLOAD for runs specified in the metadata file:\n\n```bash\nassembly_manifest\n --study STUDY raw reads study ID\n --data DATA metadata CSV - run_id, coverage, assembler, version, filepath\n --assembly_study ASSEMBLY_STUDY\n pre-existing study ID to submit to if available. Must exist in the webin account\n --force overwrite all existing manifests\n```\n\n## Upload assemblies\n\nOnce manifest files are generated, it is necessary to use ENA's webin-cli resource to upload genomes.\n\nTo test your submission add the `-test` argument.\n\nA live execution example within this repo is the following:\n```bash\nena-webin-cli \\\n -context=genome \\\n -manifest=SRR12240187.manifest \\\n -userName=$ENA_WEBIN \\\n -password=$ENA_WEBIN_PASSWORD \\\n -submit\n```\n\nMore information on ENA's webin-cli can be found [here](<https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html>).\n",
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