Askocli

AskOcli allow an AskOmics user to integrate file with the command line into a distant AskOmics.

Requirment

• python3
• python3-venv

Installation

Install from pip

pip install askocli

Or from sources;

Clone the repository

git clone https://github.com/askomics/askocli.git
cd askocli

Set up and activate a virtual environment:

python3 -m venv venv
source venv/bin/activate

Install the script in the virtual environment:

python3 setup.py install

Usage example

Integration

askocli integrate -a http://localhost:6543 -k mYap1Key path/to/file.csv
askocli integrate -a http://localhost:6543 -k mYap1Key -e gene transcript -t Arabidopsis_thaliana path/to/file.gff
askocli integrate -a http://localhost:6543 -k mYap1Key path/to/file.ttl

History

• 0.1: Initial release!
  • Integrate CSV file into a distant AskOmics
• 0.2:
  • Use API key instead of password
  • Integrate GFF and TTL
• 0.3: APIkey
  • Use only the API key without the username to login
  • Better error managment
  • Option -c, --columns to force the columns types
  • Option --key-columns to set the key columns
  • Option --public to integrate public data
  • Option --disabled-columns to don't integrate a columns of a TSV
• 0.3.2
  • FIX error message
• 0.4: Bed files integration
  • Integration of Bed files
  • Option --uri to specify an uri for the entity
  • Option --headers to set custom headers for TSV files
• 0.5: Compatibility with AskOmics 19.01.2