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Description: using configuration files that are in /etc or in ~/.sepp
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2020-10-08
--- a/sepp/config.py
+++ b/sepp/config.py
@@ -49,11 +49,11 @@
_LOG = get_logger(__name__)
-root_p = open(os.path.join(os.path.split(
- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()
-print("root_p='%s'" % root_p)
-main_config_path = os.path.join(root_p, "main.config")
-
+home = os.path.expanduser("~")
+if os.path.isfile(home + "/.sepp/sepp.config"):
+ main_config_path = home + "/.sepp/sepp.config"
+else:
+ main_config_path = "/etc/sepp/sepp.config"
def set_main_config_path(filename):
global main_config_path
--- a/sepp/ensemble.py
+++ b/sepp/ensemble.py
@@ -163,7 +163,11 @@
def augment_parser():
- sepp.config.set_main_config_path(os.path.expanduser("~/.sepp/upp.config"))
+ home = os.path.expanduser("~")
+ if os.path.isfile(home + "/.sepp/upp.config"):
+ sepp.config.set_main_config_path(home + "/.sepp/upp.config")
+ else:
+ sepp.config.set_main_config_path("/etc/sepp/upp.config")
parser = sepp.config.get_parser()
parser.description = (
"This script runs the UPP algorithm on set of sequences. A backbone "
--- a/sepp/exhaustive_upp.py
+++ b/sepp/exhaustive_upp.py
@@ -382,9 +382,11 @@
def augment_parser():
- root_p = open(os.path.join(os.path.split(
- os.path.split(__file__)[0])[0], "home.path")).readlines()[0].strip()
- upp_config_path = os.path.join(root_p, "upp.config")
+ home = os.path.expanduser("~")
+ if os.path.isfile(home + "/.sepp/upp.config"):
+ upp_config_path = home + "/.sepp/upp.config"
+ else:
+ upp_config_path = "/etc/sepp/upp.config"
sepp.config.set_main_config_path(upp_config_path)
parser = sepp.config.get_parser()
parser.description = (
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