1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d2fc633d1bcc/
Changeset: d2fc633d1bcc
Branch: stable
User: BjoernGruening
Date: 2014-08-13 14:56:37
Summary: Adding missing imports.
Affected #: 1 file
diff -r 7e81cbc2603f0695802ab49dcd65f6dda7b42322 -r d2fc633d1bcc2d02c5efccf923c4e3ce5336512a lib/tool_shed/galaxy_install/repair_repository_manager.py
--- a/lib/tool_shed/galaxy_install/repair_repository_manager.py
+++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py
@@ -1,5 +1,6 @@
+import os
+import tempfile
import logging
-import os
log = logging.getLogger( __name__ )
@@ -7,6 +8,8 @@
from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
from tool_shed.galaxy_install.tools import tool_panel_manager
+from tool_shed.util import hg_util
+from tool_shed.util import basic_util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import shed_util_common as suc
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d30b580ffbc5/
Changeset: d30b580ffbc5
User: greg
Date: 2014-08-12 20:15:00
Summary: Do not include invalid tools when checking for "orphan" tool dependencies in the Tool Shed.
Affected #: 1 file
diff -r 264657dfe72d2aa1c2ec1f5ff1aa1f5c1ac16f91 -r d30b580ffbc5cdb5f9fe8fcefe7261152fab1303 lib/tool_shed/galaxy_install/dependency_display.py
--- a/lib/tool_shed/galaxy_install/dependency_display.py
+++ b/lib/tool_shed/galaxy_install/dependency_display.py
@@ -153,7 +153,7 @@
# Updating should cause no problems here since a tool dependency cannot be included
# in both dictionaries.
tool_dependencies.update( orphan_tool_dependencies )
- if tool_dependencies and ( tools or invalid_tools ):
+ if tool_dependencies and tools:
for td_key, requirements_dict in tool_dependencies.items():
if td_key == 'set_environment':
# "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}]
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3aad77adffba/
Changeset: 3aad77adffba
User: dannon
Date: 2014-08-12 17:28:08
Summary: Update tool_list.py to indicate the correct tool_conf.xml (not sample)
Affected #: 1 file
diff -r 18e8ddfb9c3c7407daae21b49d64300e4edf7cc4 -r 3aad77adffba5e3cbb8910ca21387c3effefc429 tool_list.py
--- a/tool_list.py
+++ b/tool_list.py
@@ -1,6 +1,6 @@
import os,sys
-#--------read tool_conf.xml.sample to get all the tool xml file names-----------
+#--------read tool_conf.xml to get all the tool xml file names-----------
onoff = 1
tool_list = []
for line in open("tool_conf.xml", "r"):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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