Metadata-Version: 2.1
Name: ena-upload-cli
Version: 0.1.2
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: # 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**)
        
        ## The tool dependencies in LINUX
        
        * curl
        * Genshi
        * subprocess
        * shlex
        * json
        * argparse
        * hashlib
        * ftplib
        * uuid
        * datetime
        * lxml
        * pandas
        
        ## Installation
        
        ```
        pip install ena-upload-cli
        ```
        
        ## Test the tool
        
        **This is still a developmental version, please run the tool in the program directory for now.**
        
        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 command: **add metadata and sequence data**
        
         `python ena_upload.py --action add --center 'your_center_name' --webin_id your_id --password your_password --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`
        
         test command: **modify a metadata**
        
         `python ena_upload.py --action modify --center 'your_center_name' --webin_id your_id --password your_password --study example_tables/ENA_template_studies-2020-05-01T14\:21.tsv`
        
Keywords: pip,ena-upload-cli,cli,ENA,upload
Platform: UNKNOWN
Classifier: Operating System :: OS Independent
Requires-Python: >=2.7
Description-Content-Type: text/markdown
