1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/9f6a7491fae8/
changeset: r5505:9f6a7491fae8
user: natefoo
date: 2011-05-06 18:09:58
summary: Fix a typo in the sample tool_conf.xml, thanks Marina Gourtovaia.
affected #: 1 file (1 byte)
--- a/tool_conf.xml.sample Fri May 06 11:49:02 2011 -0400
+++ b/tool_conf.xml.sample Fri May 06 12:09:58 2011 -0400
@@ -319,7 +319,7 @@
<section name="NGS: Indel Analysis" id="indel_analysis"><tool file="indels/sam_indel_filter.xml" /><tool file="indels/indel_sam2interval.xml" />
- <tool file="indels/indel_table.xml" />"
+ <tool file="indels/indel_table.xml" /><tool file="indels/indel_analysis.xml" /></section><section name="NGS: RNA Analysis" id="ngs-rna-tools">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/2f2a223f1dde/
changeset: r5504:2f2a223f1dde
user: natefoo
date: 2011-05-06 17:49:02
summary: Standardize naming of reserved/predefined values in the param_dict. Old values are maintaned as well.
affected #: 2 files (156 bytes)
--- a/lib/galaxy/jobs/__init__.py Fri May 06 10:28:54 2011 -0400
+++ b/lib/galaxy/jobs/__init__.py Fri May 06 11:49:02 2011 -0400
@@ -352,8 +352,8 @@
else:
userId = 'Anonymous'
userEmail = 'Anonymous'
- incoming['userId'] = userId
- incoming['userEmail'] = userEmail
+ incoming['__user_id__'] = incoming['userId'] = userId
+ incoming['__user_email__'] = incoming['userEmail'] = userEmail
# Build params, done before hook so hook can use
param_dict = self.tool.build_param_dict( incoming, inp_data, out_data, self.get_output_fnames(), self.working_directory )
# Certain tools require tasks to be completed prior to job execution
--- a/lib/galaxy/tools/__init__.py Fri May 06 10:28:54 2011 -0400
+++ b/lib/galaxy/tools/__init__.py Fri May 06 11:49:02 2011 -0400
@@ -1514,11 +1514,11 @@
param_dict['__new_file_path__'] = os.path.abspath(self.app.config.new_file_path)
# The following points to location (xxx.loc) files which are pointers
# to locally cached data
- param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path
+ param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path
# For the upload tool, we need to know the root directory and the
# datatypes conf path, so we can load the datatypes registry
- param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
- param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( self.app.config.datatypes_config )
+ param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root )
+ param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = os.path.abspath( self.app.config.datatypes_config )
# Return the dictionary of parameters
return param_dict
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/551e6526954a/
changeset: r5503:551e6526954a
user: guru
date: 2011-05-06 16:28:54
summary: Commented out 'Wavelet analysis' section from tool_conf.xml.sample - will be reverted once functional tests are written for these tools.
affected #: 1 file (87 bytes)
--- a/tool_conf.xml.sample Thu May 05 19:05:39 2011 -0400
+++ b/tool_conf.xml.sample Fri May 06 10:28:54 2011 -0400
@@ -146,12 +146,15 @@
<label text="GFF" id="gff" /><tool file="stats/count_gff_features.xml" /></section>
+ <!--
+ Keep this section commented until all of the tools have functional tests
<section name="Wavelet Analysis" id="dwt"><tool file="discreteWavelet/execute_dwt_IvC_all.xml" /><tool file="discreteWavelet/execute_dwt_cor_aVa_perClass.xml" /><tool file="discreteWavelet/execute_dwt_cor_aVb_all.xml" /><tool file="discreteWavelet/execute_dwt_var_perClass.xml" /></section>
+ --><section name="Graph/Display Data" id="plots"><tool file="plotting/histogram2.xml" /><tool file="plotting/scatterplot.xml" />
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/4ba34b095a79/
changeset: r5502:4ba34b095a79
user: jgoecks
date: 2011-05-06 01:05:39
summary: Trackster: use GTF metadata to create dynamic filters.
affected #: 1 file (448 bytes)
--- a/lib/galaxy/visualization/tracks/data_providers.py Thu May 05 16:51:56 2011 -0400
+++ b/lib/galaxy/visualization/tracks/data_providers.py Thu May 05 19:05:39 2011 -0400
@@ -394,6 +394,14 @@
filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ]
filter_col += 1
if isinstance( self.original_dataset.datatype, Gtf ):
+ # Create filters based on dataset metadata.
+ for name, a_type in self.original_dataset.metadata.attribute_types.items():
+ if a_type in [ 'int', 'float' ]:
+ filters.append( { 'name': name, 'type': a_type, 'index': filter_col } )
+ filter_col += 1
+
+ '''
+ # Old code: use first line in dataset to find attributes.
for i, line in enumerate( open(self.original_dataset.file_name) ):
if not line.startswith('#'):
# Look at first line for attributes and types.
@@ -411,10 +419,11 @@
filters.append( { 'name': attr, 'type': attr_type, 'index': filter_col } )
filter_col += 1
break
+ '''
elif isinstance( self.original_dataset.datatype, Bed ):
# Can filter by score column only.
filters = [ { 'name': 'Score', 'type': 'int', 'index': filter_col } ]
-
+
return filters
class TabixDataProvider( FilterableMixin, TracksDataProvider ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/a0165dfc5664/
changeset: r5496:a0165dfc5664
user: jgoecks
date: 2011-05-03 15:45:40
summary: Fix bug in 'Filter GTF data by attribute values list' tool.
affected #: 1 file (41 bytes)
--- a/tools/filters/gff/gtf_filter_by_attribute_values_list.py Mon May 02 17:35:06 2011 -0400
+++ b/tools/filters/gff/gtf_filter_by_attribute_values_list.py Tue May 03 09:45:40 2011 -0400
@@ -54,7 +54,7 @@
for line in open( gff_file ):
fields = line.split( '\t' )
attributes = parse_gff_attributes( fields[8] )
- if attributes[ attribute_name ] in ids_dict:
+ if ( attribute_name in attributes ) and ( attributes[ attribute_name ] in ids_dict ):
output.write( line )
output.close()
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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