diff --git a/lib/galaxy/web/controllers/genetrack.py b/lib/galaxy/web/controllers/genetrack.py
index 019239d0da3..b3264b0954a 100644
--- a/lib/galaxy/web/controllers/genetrack.py
+++ b/lib/galaxy/web/controllers/genetrack.py
@@ -167,7 +167,10 @@ class WebRoot(BaseController):
param = atlas.Param( word=word )
# search for a given
- session = sql.get_session( conf.SQL_URI )
+ try:
+ session = sql.get_session( conf.SQL_URI )
+ except:
+ return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id)
if param.word:
def search_query( word, text ):
@@ -208,7 +211,11 @@ class WebRoot(BaseController):
FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20),
PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20),
)
- session = sql.get_session( conf.SQL_URI )
+
+ try:
+ session = sql.get_session( conf.SQL_URI )
+ except:
+ return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id)
if os.path.exists( conf.HDF_DATABASE ):
db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' )
diff --git a/tools/visualization/genetrack.xml b/tools/visualization/genetrack.xml
index 8ab46560391..d48d4999953 100644
--- a/tools/visualization/genetrack.xml
+++ b/tools/visualization/genetrack.xml
@@ -3,8 +3,8 @@
Track creator/viewer
-
-
+
+
genetrack.py -l $data_label
@@ -24,14 +24,14 @@
- [a-zA-Z0-9]{0,25}
+ [a-zA-Z0-9]{1,25}
-
+
- [a-zA-Z0-9]{0,25}
-
+ [a-zA-Z0-9]{1,25}
+
@@ -47,16 +47,27 @@
numpy
-This tool takes the input Fit Data and creates a peak and curve plot showing
-the reads and fitness on each basepair. Features can be plotted below as tracks.
+This tool takes the input Fit Data and creates a peak and curve plot
+showing the reads and fitness on each basepair. Features can be
+plotted below as tracks. Fit data is coverage output from tools like
+the Lastz tool. Features are simply interval datasets that may be
+plotted as tracks below the optional fit data. Both the fit data and
+feature datasets are optional, but at least one of either is required
+to generate a track.
-----
**Syntax**
- **Track Label** is the name of the generated track.
-- **Fit Data** are the datasets to calculate coverage/reads across basepairs and generate a curve.
-- **Features** are additional datasets (interval format) to be plotted below as tracks.
+
+- **Fit Data** is the dataset to calculate coverage/reads across
+ basepairs and generate a curve. This is optional, and tracks may
+ be created simply showing features.
+
+- **Features** are datasets (interval format) to be plotted as tracks.
+ These are also optional, but at least 1 feature track or 1 fit
+ data is required to generate a track.
diff --git a/tools/visualization/genetrack_code.py b/tools/visualization/genetrack_code.py
index 9c20ec27b73..b79f77b13ce 100644
--- a/tools/visualization/genetrack_code.py
+++ b/tools/visualization/genetrack_code.py
@@ -10,4 +10,3 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=No
out_data['genetrack'].metadata.label = param_dict['data_label']
out_data['genetrack'].info = "Use the link below to view the custom track."
out_data['bed_out'].info = ""
-
\ No newline at end of file