2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c77d83fe4c3e/
Changeset: c77d83fe4c3e
Branch: next-stable
User: jeremy goecks
Date: 2014-01-30 21:54:26
Summary: Fix bug that prevented relative path from being used for len_file_path config
option.
Affected #: 2 files
diff -r fd4936ae82193639011ed06b9552ec1a8c8166e5 -r
c77d83fe4c3e37d07c241bb1f76064a3d0b7f149 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -67,7 +67,7 @@
self.enable_unique_workflow_defaults = string_as_bool( kwargs.get(
'enable_unique_workflow_defaults', False ) )
self.tool_path = resolve_path( kwargs.get( "tool_path",
"tools" ), self.root )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path",
"tool-data" ), os.getcwd() )
- self.len_file_path = kwargs.get( "len_file_path",
resolve_path(os.path.join(self.tool_data_path,
'shared','ucsc','chrom'), self.root) )
+ self.len_file_path = resolve_path( kwargs.get( "len_file_path",
os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ),
self.root )
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ),
self.root )
# The value of migrated_tools_config is the file reserved for containing only
those tools that have been eliminated from the distribution
# and moved to the tool shed.
diff -r fd4936ae82193639011ed06b9552ec1a8c8166e5 -r
c77d83fe4c3e37d07c241bb1f76064a3d0b7f149 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -236,7 +236,7 @@
if not chrom_info:
# Default to built-in build.
chrom_info = os.path.join( trans.app.config.len_file_path,
"%s.len" % input_dbkey )
- incoming[ "chromInfo" ] = chrom_info
+ incoming[ "chromInfo" ] = os.path.abspath( chrom_info )
inp_data.update( db_datasets )
# Determine output dataset permission/roles list
https://bitbucket.org/galaxy/galaxy-central/commits/72a210496cda/
Changeset: 72a210496cda
User: jeremy goecks
Date: 2014-01-30 21:54:54
Summary: Automated merge of next-stable to default branch
Affected #: 2 files
diff -r bf7251133a037cda8ca7025a15af4ab9efb326ba -r
72a210496cda233f28769dac11c116e0e6a71f18 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -67,7 +67,7 @@
self.enable_unique_workflow_defaults = string_as_bool( kwargs.get(
'enable_unique_workflow_defaults', False ) )
self.tool_path = resolve_path( kwargs.get( "tool_path",
"tools" ), self.root )
self.tool_data_path = resolve_path( kwargs.get( "tool_data_path",
"tool-data" ), os.getcwd() )
- self.len_file_path = kwargs.get( "len_file_path",
resolve_path(os.path.join(self.tool_data_path,
'shared','ucsc','chrom'), self.root) )
+ self.len_file_path = resolve_path( kwargs.get( "len_file_path",
os.path.join( self.tool_data_path, 'shared','ucsc','chrom') ),
self.root )
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ),
self.root )
# The value of migrated_tools_config is the file reserved for containing only
those tools that have been eliminated from the distribution
# and moved to the tool shed.
diff -r bf7251133a037cda8ca7025a15af4ab9efb326ba -r
72a210496cda233f28769dac11c116e0e6a71f18 lib/galaxy/tools/actions/__init__.py
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -236,7 +236,7 @@
if not chrom_info:
# Default to built-in build.
chrom_info = os.path.join( trans.app.config.len_file_path,
"%s.len" % input_dbkey )
- incoming[ "chromInfo" ] = chrom_info
+ incoming[ "chromInfo" ] = os.path.abspath( chrom_info )
inp_data.update( db_datasets )
# Determine output dataset permission/roles list
Repository URL:
https://bitbucket.org/galaxy/galaxy-central/
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