Metadata-Version: 2.1
Name: ena-upload-cli
Version: 0.2.5
Summary: Command Line Interface to upload data to the European Nucleotide Archive
Home-page: https://github.com/usegalaxy-eu/ena-upload-cli
Author: Dilmurat Yusuf
Author-email: bjoern.gruening@gmail.com
License: MIT
Description: [![Python application](https://github.com/usegalaxy-eu/ena-upload-cli/workflows/Python%20application/badge.svg)](https://github.com/usegalaxy-eu/ena-upload-cli/actions?query=workflow%3A%22Python+application%22)
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        # ENA upload tool
        
        ## About
        
        The program submits experimental data and respective metadata to the European Nucleotide Archive (ENA). The metadata should be provided in separate tables corresponding to the following ENA objects:
        
        * STUDY
        * SAMPLE
        * EXPERIMENT
        * RUN
        
        The program to perform the following actions:
        
        * add: add an object to the archive
        * modify: modify an object in the archive
        * cancel: cancel a private object and its dependent objects (**under development**)
        * release: release a private object immediately to the public (**under development**)
        
        ## Tool dependencies
        
        * curl
        * python 2.7+ including following packages:
          * Genshi
          * lxml
          * pandas
        
        ## Installation
        
        ```
        pip install ena-upload-cli
        ```
        
        > Be aware that Windows can give problems with the `curl` commands executed by the script. Check that curl is available in your PATH.
        
        ## Usage
        
        ```
        Minimal:  ena-upoad-cli --action {add,modify,cancel,release} --center CENTER_NAME  --secret SECRET
        
        All supported arguments:
          -h, --help            show this help message and exit
          --action {add,modify,cancel,release}
                                 add: add an object to the archive
                                 modify: modify an object in the archive
                                 cancel: cancel a private object and its dependent objects
                                 release: release a private object immediately to public
          --study STUDY         table of STUDY object
          --sample SAMPLE       table of SAMPLE object
          --experiment EXPERIMENT
                                table of EXPERIMENT object
          --run RUN             table of RUN object
          --data [FILE [FILE ...]]
                                data for submission
          --center CENTER_NAME  specific to your Webin account
          --tool TOOL_NAME      Specify the name of the tool this submission is done with. Default: ena-upload-cli
          --tool_version TOOL_VERSION
                                Specify the version of the tool this submission is done with.
          --secret SECRET       .secret file containing the password of your Webin account
          -d, --dev             Flag to use the dev/sandbox endpoint of ENA.
          --vir                 Flag to use the viral sample template.
        ```
        
        Mandatory arguments: --action, --center and --secret.
        
        ### ENA Webin
        
        A Webin can be made [here](https://www.ebi.ac.uk/ena/submit/sra/#home) if you don't have one already. The *--webin_id* parameter makes use of the full username looking like: `Webin-XXXXX`. Visit [Webin online](https://www.ebi.ac.uk/ena/submit/webin) to check on your submissions or [dev Webin](https://wwwdev.ebi.ac.uk/ena/submit/webin) to check on test submissions.
        
        ### The .secret.yml file
        
        To avoid exposing your credentials through the terminal history, it is recommended to make use of a `.secret.yml` file, containing your password and username keywords. An example is given in the root of this directory.
        
        
        ### dev instance
        
        
        By default the submission will be done using following url to ENA: https://www.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA
        
        Use the *--dev* flag if you want to do a test submission using the tool by the sandbox dev instance of ENA: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA. A TEST submission will be discarded within 24 hours.
        
        ### The data files
        
        **Supported data**
        
        - [x] Read data
        - [ ] Genome Assembly
        - [ ] Transcriptome Assembly
        - [x] Template Sequence
        - [x] Other Analyses
        
        
        Most files uploaded to the ENA FTP server need to be compressed.
        
        More information on how ENA wants to receive the files can be found [here](https://ena-docs.readthedocs.io/en/latest/submit/fileprep/preparation.html).
        
        
        ## Tool overview
        
        inputs:
        * metadata tables
          * examples in `example_table`
          * Please define actions in **status** column e.g. `add`, `modify`, cancel, release
          * to perform bulk submission of all objects, the `aliases ids` in different ENA objects should be in the association where alias ids in experiment object link all objects together
        * experimental data
          * examples in `example_data`
        
        outputs:
        * In the same directory of inputs
        * metadata tables with updated info in `status` and other relevant columns, e.g:
          * updated status: `added`, `modified`, canceled, released
          * accession ids
          * submission date
        
        ## Test the tool
        
        test command: **add metadata and sequence data**
        
         ```
         ena_upload --action add --center 'your_center_name' --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --secret .secret.yml
         ```
        
         test command: **modify metadata**
        
         ```
         ena_upload --action modify --center 'your_center_name' --study example_tables/ENA_template_studies-2020-05-01T1421.tsv --dev --secret .secret.yml
         ```
        
        test command for **viral data**
        
         ```
         ena_upload --action add --center 'your_center_name' --study example_tables/ENA_template_studies.tsv --sample example_tables/ENA_template_samples_vir.tsv --experiment example_tables/ENA_template_experiments.tsv --run example_tables/ENA_template_runs.tsv --data example_data/*gz --dev --vir --secret .secret.yml
         ```
        
Keywords: pip,ena-upload-cli,cli,ENA,upload
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Requires-Python: >=2.7
Description-Content-Type: text/markdown
