Package Biskit :: Module settings

Module settings

Settings

This module provides global settings as fields. Throughout Biskit a (environment-dependent) parameter such as, e.g., ssh_bin can be addressed as:

>>> import Biskit.settings as S
>>> bin = S.ssh_bin

However, since a user should not be required to hack python modules, ssh_bin is not actually defined in settings.py. Instead, the value is taken from ~/.biskit/settings.cfg -- which should have an entry like ssh_bin=/bin/ssh # comment. If this entry (or the config file) is not found, settings.py uses the default value from biskit/external/defaults/settings.cfg.

If missing, the user configuration file ~/.biskit/settings.cfg is created automatically during the startup of Biskit (i.e. for any import). The auto-generated file only contains parameters for which the default values don't seem to work (invalid paths or binaries).

See Biskit.SettingsManager

Summary for Biskit users

If you want to change a biskit parameter, do so in ~/.biskit/settings.cfg

Summary for Biskit developpers

If you want to create a new user-adjustable parameter, do so in biskit/external/defaults/settings.cfg.

Summary for all

!Dont't touch settings.py!

Variables

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python_bin = sys.executable

xterm_bin = T.absbinary('xterm')

projectRoot = T.projectRoot()

pymol_scripts = projectRoot+ '/external/pymol/'

env = {}

blast_env = {'BLASTDB': '/home/Bis/raik/data/prog/blast/db', 'BL...

amber_env = {'AMBERHOME_8': '/Bis/shared/rh73/amber8_intel-7.1'}

Variables Details

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python_bin

Value:

sys.executable

xterm_bin

Value:

T.absbinary('xterm')

projectRoot

Value:

T.projectRoot()

pymol_scripts

Value:

projectRoot+ '/external/pymol/'

env

Value:

{}

blast_env

Value:

{'BLASTDB': '/home/Bis/raik/data/prog/blast/db', 'BLASTMA': '/home/Bis
/johan/APPLICATIONS/blast'}

amber_env

Value:

{'AMBERHOME_8': '/Bis/shared/rh73/amber8_intel-7.1'}