1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/5c7333bb427f/
changeset: 5c7333bb427f
user: jgoecks
date: 2011-10-18 01:57:54
summary: Better handling of reference data in Trackster read tracks.
affected #: 1 file (-1 bytes)
--- a/static/scripts/trackster.js Mon Oct 17 17:41:10 2011 -0400
+++ b/static/scripts/trackster.js Mon Oct 17 19:57:54 2011 -0400
@@ -4375,7 +4375,7 @@
var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) {
FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
- this.ref_seq = ref_seq;
+ this.ref_seq = (ref_seq ? ref_seq.data : null);
};
ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false });
@@ -4410,8 +4410,7 @@
tile_region = [tile_low, tile_high],
base_offset = 0,
seq_offset = 0,
- gap = 0
- ref_seq = this.ref_seq.data,
+ gap = 0,
char_width_px = ctx.canvas.manager.char_width_px;
// Keep list of items that need to be drawn on top of initial drawing layer.
@@ -4465,8 +4464,8 @@
// TODO: this can be made much more efficient by computing the complete sequence
// to draw and then drawing it.
for (var c = 0, str_len = seq.length; c < str_len; c++) {
- if (this.prefs.show_differences && ref_seq) {
- var ref_char = ref_seq[seq_start - tile_low + c];
+ if (this.prefs.show_differences && this.ref_seq) {
+ var ref_char = this.ref_seq[seq_start - tile_low + c];
if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) {
continue;
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2fed8f8737cd/
changeset: 2fed8f8737cd
user: natefoo
date: 2011-10-17 20:19:34
summary: PBS cluster error user messages now suggest retrying the job.
affected #: 1 file (-1 bytes)
--- a/lib/galaxy/jobs/runners/pbs.py Mon Oct 17 13:49:06 2011 -0400
+++ b/lib/galaxy/jobs/runners/pbs.py Mon Oct 17 14:19:34 2011 -0400
@@ -292,7 +292,7 @@
if not job_id:
errno, text = pbs.error()
log.debug( "(%s) pbs_submit failed, PBS error %d: %s" % (galaxy_job_id, errno, text) )
- job_wrapper.fail( "Unable to run this job due to a cluster error" )
+ job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" )
return
if pbs_queue_name is None:
@@ -419,7 +419,7 @@
assert int( status.exit_status ) == 0
log.debug("(%s/%s) PBS job has completed successfully" % ( galaxy_job_id, job_id ) )
except AssertionError:
- pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error. Please retry or'
+ pbs_job_state.fail_message = 'Job cannot be completed due to a cluster error, please retry it later'
log.error( '(%s/%s) PBS job failed: %s' % ( galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), 'Unknown error: %s' % status.exit_status ) ) )
self.work_queue.put( ( 'fail', pbs_job_state ) )
continue
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/be6c89c33639/
changeset: be6c89c33639
user: greg
date: 2011-10-17 19:49:06
summary: Fix for loading a workflow that contains tools whose tools ids are the old version of tools ids, but whose available tools use the new tool guids as the tool id because the tools were installed from a Galaxy tool shed.
affected #: 1 file (-1 bytes)
--- a/lib/galaxy/workflow/modules.py Mon Oct 17 12:22:27 2011 -0400
+++ b/lib/galaxy/workflow/modules.py Mon Oct 17 13:49:06 2011 -0400
@@ -209,9 +209,18 @@
@classmethod
def from_workflow_step( Class, trans, step ):
tool_id = step.tool_id
+ install_tool_id = None
if tool_id not in trans.app.toolbox.tools_by_id:
- return None
- else:
+ for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items():
+ if available_tool_id.find( tool_id ) >=0:
+ # We're attempting to match tool id against a tool guid.
+ # TODO: match by tool_id (and version if we attempt that, but
+ # workflows will break) is not good enough because
+ # 2 tools installed from a tool shed could both match this. We
+ # need to present a select list here.
+ install_tool_id = available_tool_id
+ break
+ if tool_id in trans.app.toolbox.tools_by_id or install_tool_id:
module = Class( trans, tool_id )
module.state = DefaultToolState()
module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True )
@@ -223,6 +232,7 @@
pjadict[pja.action_type] = pja
module.post_job_actions = pjadict
return module
+ return None
def save_to_step( self, step ):
step.type = self.type
step.tool_id = self.tool_id
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.