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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