1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/e005f2009645/ changeset: r5062:e005f2009645 user: kanwei date: 2011-02-15 19:53:16 summary: Add len_file_path configurable to specify where chrom .len files are stored affected #: 4 files (322 bytes)
--- a/lib/galaxy/config.py Tue Feb 15 13:38:22 2011 -0500 +++ b/lib/galaxy/config.py Tue Feb 15 13:53:16 2011 -0500 @@ -46,6 +46,7 @@ self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', 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.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
--- a/lib/galaxy/web/base/controller.py Tue Feb 15 13:38:22 2011 -0500 +++ b/lib/galaxy/web/base/controller.py Tue Feb 15 13:53:16 2011 -0500 @@ -130,7 +130,7 @@
# Read len files. if not self.len_files: - len_files = glob.glob(os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "*.len" )) + len_files = glob.glob( os.path.join(trans.app.config.len_file_path, "*.len") ) self.len_files = [ os.path.split(f)[1].split(".len")[0] for f in len_files ] # get xxx.len
user_keys = {}
--- a/lib/galaxy/web/controllers/tracks.py Tue Feb 15 13:38:22 2011 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Feb 15 13:53:16 2011 -0500 @@ -306,7 +306,7 @@ if not len_file: len_ds = trans.db_dataset_for( dbkey ) if not len_ds: - len_file = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % vis_dbkey ) + len_file = os.path.join( trans.app.config.len_file_path, "%s.len" % vis_dbkey ) else: len_file = len_ds.file_name
--- a/universe_wsgi.ini.sample Tue Feb 15 13:38:22 2011 -0500 +++ b/universe_wsgi.ini.sample Tue Feb 15 13:53:16 2011 -0500 @@ -132,6 +132,10 @@ # http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration #tool_data_path = tool-data
+# Directory where chrom len files are kept, currently mainly used by trackster +#len_file_path = tool-data/shared/ucsc/chrom + + # Datatypes config file, defines what data (file) types are available in # Galaxy. #datatypes_config_file = datatypes_conf.xml
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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