From 4cade4941913166d2fda26be1df6617291a67d48 Mon Sep 17 00:00:00 2001 From: Kanwei Li Date: Tue, 15 Feb 2011 13:53:16 -0500 Subject: [PATCH] Add len_file_path configurable to specify where chrom .len files are stored --- lib/galaxy/config.py | 1 + lib/galaxy/web/base/controller.py | 2 +- lib/galaxy/web/controllers/tracks.py | 2 +- universe_wsgi.ini.sample | 4 ++++ 4 files changed, 7 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 4a2b241b58a..f5783ef9747 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -46,6 +46,7 @@ class Configuration( object ): 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 ) diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py index fef3ce8f587..3b133692064 100644 --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -130,7 +130,7 @@ class UsesVisualization( SharableItemSecurity ): # 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 = {} diff --git a/lib/galaxy/web/controllers/tracks.py b/lib/galaxy/web/controllers/tracks.py index 7ed563ee340..a1d2857e452 100644 --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -306,7 +306,7 @@ class TracksController( BaseController, UsesVisualization, UsesHistoryDatasetAss 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 diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample index eba12617ea8..4068af64f3f 100644 --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -132,6 +132,10 @@ paste.app_factory = galaxy.web.buildapp:app_factory # 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