1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/93d2916499f4/
Changeset: 93d2916499f4
User: natefoo
Date: 2015-02-12 16:47:58+00:00
Summary: Ensure the correct default Galaxy config file is found in common_startup.sh, it
makes a difference for egg fetching since some eggs are conditional based on
config.
Affected #: 1 file
diff -r 51a3606fe3bdf21d663b35d41c886ff819fd234d -r 93d2916499f4ddc3093adc65cb5718a25841aa15 scripts/common_startup.sh
--- a/scripts/common_startup.sh
+++ b/scripts/common_startup.sh
@@ -34,7 +34,13 @@
done
fi
-: ${GALAXY_CONFIG_FILE:=config/galaxy.ini.sample}
+: ${GALAXY_CONFIG_FILE:=config/galaxy.ini}
+if [ ! -f $GALAXY_CONFIG_FILE ]; then
+ GALAXY_CONFIG_FILE=universe_wsgi.ini
+fi
+if [ ! -f $GALAXY_CONFIG_FILE ]; then
+ GALAXY_CONFIG_FILE=config/galaxy.ini.sample
+fi
if [ $FETCH_EGGS -eq 1 ]; then
python ./scripts/check_eggs.py -q -c $GALAXY_CONFIG_FILE
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f1c89c016624/
Changeset: f1c89c016624
Branch: stable
User: natefoo
Date: 2015-02-12 14:00:26+00:00
Summary: Update tag latest_2015.01.13 for changeset 577b270034b4
Affected #: 1 file
diff -r 577b270034b48d90e58ffbea296e700d229545c9 -r f1c89c016624edd48edf604b14745d2a85b8402a .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -22,4 +22,4 @@
2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06
782fa60fc65488aea0c618d723e9a63d42caf865 latest_2014.10.06
2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13
-644deef1a5789b788552a6db7f3d6fe07d81c79d latest_2015.01.13
+577b270034b48d90e58ffbea296e700d229545c9 latest_2015.01.13
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1a4a65522d02/
Changeset: 1a4a65522d02
User: dannon
Date: 2015-02-12 12:57:51+00:00
Summary: Fix at least one error with zipfile downloads and file permissions not being set correctly.
Affected #: 1 file
diff -r 10a1ea8d9e153bd1abe30de07a64d3d043601889 -r 1a4a65522d02834212a3e05487ae1e97071bb6be lib/galaxy/eggs/__init__.py
--- a/lib/galaxy/eggs/__init__.py
+++ b/lib/galaxy/eggs/__init__.py
@@ -463,7 +463,7 @@
try:
for info in z.infolist():
name = info.filename
- perm = (info.external_attr >> 16L) & 0777
+ mode = (info.external_attr >> 16L) & 0777
# don't extract absolute paths or ones with .. in them
if name.startswith('/') or '..' in name:
continue
https://bitbucket.org/galaxy/galaxy-central/commits/5b2f1eab2819/
Changeset: 5b2f1eab2819
User: dannon
Date: 2015-02-12 13:28:37+00:00
Summary: Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers.
Affected #: 1 file
diff -r 1a4a65522d02834212a3e05487ae1e97071bb6be -r 5b2f1eab281920eca6c9d1b84e6cebf02866ea09 scripts/fetch_eggs.py
--- a/scripts/fetch_eggs.py
+++ b/scripts/fetch_eggs.py
@@ -32,7 +32,7 @@
root.addHandler( logging.StreamHandler( sys.stdout ) )
lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) )
-sys.path.append( lib )
+sys.path.insert(1, lib)
from galaxy.eggs import Crate, EggNotFetchable
import pkg_resources
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.