Module settings
source code
Settings
This module provides Mod-global settings as fields. Throughout
Biskit.Mod a (environment-dependent) parameter such as, e.g., ssh_bin
can be addressed as:
>>> import Biskit.Mod.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_Mod.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_Mod.cfg.
If missing, the user configuration file
~/.biskit/settings_Mod.cfg is created automatically during
the startup of Biskit.Mod (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_Mod.cfg
Summary for Biskit developpers
If you want to create a new user-adjustable parameter, do so in
biskit/external/defaults/settings_Mod.cfg.
Summary for all
!Dont't touch settings.py!
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env = {}
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net_env = {'http_proxy': 'http://cache.pasteur.fr:8080'}
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net_ncbi = {'BLASTDB': '/Bis/db/blastdb', 'BLASTMAT': '/Bis/sha...
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net_env
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- Value:
{'http_proxy': 'http://cache.pasteur.fr:8080'}
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net_ncbi
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- Value:
{'BLASTDB': '/Bis/db/blastdb', 'BLASTMAT': '/Bis/shared/rh73/ncbi'}
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