Aspera option improvement

[tseemann]

Thanks for adding the --aspera option, but is very inconvient for all the users on a cluster to have to specify it, as you say "You will need to provide a path to this file every time you chose to run aspera."

Can you make the default be a file specified in an ENV variable?

For example

export ENA_ASPERA_COMMANDLINE="-m 300m -i key.ssh -DT" 
#and/or
export ENA_ASPERIA_INIFILE="/bio/sw/enaBrowserTools/etc/aspera.ini"

If either of these are set, you use them. But let -a override it.

[chrisgulvik]

os.environ.get() works the same in both py2 and py3 and the getattr() approach should as well.

If the aspera_settings.ini file is always going to be ../ from enaDataGet.py and utils.py and you wanted to save that full path as a place to check when a specific file isn't provided and env var unset, you could put a line inside utils.py enaBrowserTools_path = os.path.dirname(os.path.dirname(__file__)) then call on the utils module to get it.

Extend this if-statement:

enaBrowserTools/python3/enaDataGet.py

Lines 53 to 55 in c0911de

	if aspera_settings is not None:
	aspera = True
	utils.set_aspera_variables(aspera_settings)

elif os.environ.get('ENA_ASPERA_INIFILE'):
    aspera = True
    utils.set_aspera_variables(os.environ.get('ENA_ASPERA_INIFILE'))
elif:
    eBT_path = getattr(utils, 'enaBrowserTools_path', '')
    if os.path.exists(os.path.join(eBT_path, 'aspera_settings.ini')):
        aspera = True
        utils.set_aspera_variables(os.path.join(eBT_path, 'aspera_settings.ini'))

[nicsilvester]

I'l have a look at this. I usually try to avoid environment variables as they can be dangerous. Though given these scripts are run locally I can probably loosen that rule

[nicsilvester]

Added in v1.4 release.