encode2bag

Utility for converting ENCODE search URLs or metadata files into BDBags

Dependencies

• Python 2.7 is the minimum Python version required.
• The code and dependencies are currently compatible with Python 3.

Installation

Download the current encode2bag source code from GitHub or alternatively clone the source from GitHub if you have git installed:

git clone https://github.com/ini-bdds/encode2bag

From the root of the encode2bag source code directory execute the following command:

python setup.py install --user

Note that if you want to make encode2bag available to all users on the system, you should run the following command:

python setup.py install

If you are on a Unix-based system (including MacOS) you should execute the above command as root or use sudo.

Testing

The unit tests can be run by invoking the following command from the root of the encode2bag source code directory:

python setup.py test

Usage:

usage: encode2bag_cli.py [-h] [--url <search url>] [--metadata-file <file>]
                         [--output-name <directory name>]
                         [--output-path <path>] [--archiver {zip,tar,tgz}]
                         [--create-ro-manifest]
                         [--creator-name <person or entity name>]
                         [--creator-orcid <orcid>] [--quiet] [--debug]

Utility for converting ENCODE search URLs or metadata files into BDBags

optional arguments:
  -h, --help            show this help message and exit

  --url <search url>    Optional path to an ENCODE search url e.g., "https://w
                        ww.encodeproject.org/search/?type=Experiment&assay_tit
                        le=RNA-seq&replicates.library.biosample.biosample_type
                        =stem+cell". Either this argument or the "--metadata-
                        file" argument must be supplied.

  --metadata-file <file>
                        Optional path to a ENCODE format metadata file e.g.,
                        "metadata.tsv". Either this argument or the "--url"
                        argument must be supplied.

  --output-name <directory name>
                        Optional name for the output bag directory/bag archive
                        file. If not specified, it will automatically be
                        generated.

  --output-path <path>  Optional path to a base directory in which the bag
                        will be created. If not specified, a temporary
                        directory will be created.

  --archiver {zip,tar,tgz}
                        Archive the output bag using the specified format.

  --create-ro-manifest  Generate a Research Object compatible manifest. See
                        http://www.researchobject.org for more information.

  --creator-name <person or entity name>
                        Optional name of the person or entity responsible for
                        the creation of this bag, for inclusion in the bag
                        metadata.

  --creator-orcid <orcid>
                        Optional ORCID identifier of the bag creator, for
                        inclusion in the bag metadata.

  --quiet               Suppress logging output.

  --debug               Enable debug logging output.

For more information see: http://github.com/ini-bdds/encode2bag