1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/45735a13168b/
changeset: 45735a13168b
user: fubar
date: 2012-04-04 18:16:12
summary: Reverted picard_FastqToSam.xml which I accidentally embellished with a bogus --tmpdir flag because it does not use picard_wrapper.py
affected #: 1 file
diff -r 440e50875343ff7d48464826ce819ef5a232882a -r 45735a13168bfa54ebcf232cbd9ebc2ffe10ee92 tools/picard/picard_FastqToSam.xml
--- a/tools/picard/picard_FastqToSam.xml
+++ b/tools/picard/picard_FastqToSam.xml
@@ -4,7 +4,6 @@
<!-- Dan Blankenberg --><command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard/FastqToSam.jar"
- --tmpdir "${__new_file_path__}"
FASTQ="${input_fastq1}"
#if str( $input_fastq2) != "None":
FASTQ2="${input_fastq2}"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/440e50875343/
changeset: 440e50875343
user: jgoecks
date: 2012-04-04 17:33:26
summary: Fix bug that scrolled Trackster on double click when completely zoomed in.
affected #: 1 file
diff -r 9ceb68fe691eb50509bf95b0e7641680b993c55d -r 440e50875343ff7d48464826ce819ef5a232882a static/scripts/trackster.js
--- a/static/scripts/trackster.js
+++ b/static/scripts/trackster.js
@@ -1811,7 +1811,7 @@
}
},
zoom_in: function (point, container) {
- if (this.max_high === 0 || this.high - this.low < this.min_separation) {
+ if (this.max_high === 0 || this.high - this.low <= this.min_separation) {
return;
}
var span = this.high - this.low,
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/9ceb68fe691e/
changeset: 9ceb68fe691e
user: dannon
date: 2012-04-04 17:27:48
summary: Fix multi-input workflow selector to account for recent structural changes.
affected #: 1 file
diff -r 26403ed86d4ccf39ea88c2658012a9a99d453266 -r 9ceb68fe691eb50509bf95b0e7641680b993c55d templates/workflow/run.mako
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -37,7 +37,7 @@
placeholder = 'type to filter';
} else {
$('.multiinput').addClass('disabled');
- $('.multiinput', select.parent().prev()).removeClass('disabled');
+ $('.multiinput', select.closest('.form-row')).removeClass('disabled');
select.attr('multiple', 'multiple').attr('size', 8);
placeholder = 'type to filter, [enter] to select all';
}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/26403ed86d4c/
changeset: 26403ed86d4c
user: natefoo
date: 2012-04-04 04:07:19
summary: Allow multiple output file collection from the job_working_directory.
affected #: 4 files
diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -86,6 +86,7 @@
self.allow_user_dataset_purge = string_as_bool( kwargs.get( "allow_user_dataset_purge", "False" ) )
self.allow_user_impersonation = string_as_bool( kwargs.get( "allow_user_impersonation", "False" ) )
self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) )
+ self.collect_outputs_from = [ x.strip() for x in kwargs.get( 'collect_outputs_from', 'new_file_path,job_working_directory' ).lower().split(',') ]
self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) )
diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -443,7 +443,7 @@
# Check for and move associated_files
self.tool.collect_associated_files(out_data, self.working_directory)
# Create generated output children and primary datasets and add to param_dict
- collected_datasets = {'children':self.tool.collect_child_datasets(out_data),'primary':self.tool.collect_primary_datasets(out_data)}
+ collected_datasets = {'children':self.tool.collect_child_datasets(out_data, self.working_directory),'primary':self.tool.collect_primary_datasets(out_data, self.working_directory)}
param_dict.update({'__collected_datasets__':collected_datasets})
# Certain tools require tasks to be completed after job execution
# ( this used to be performed in the "exec_after_process" hook, but hooks are deprecated ).
diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2153,7 +2153,7 @@
shutil.rmtree(temp_file_path)
except:
continue
- def collect_child_datasets( self, output):
+ def collect_child_datasets( self, output, job_working_directory ):
"""
Look for child dataset files, create HDA and attach to parent.
"""
@@ -2161,7 +2161,12 @@
# Loop through output file names, looking for generated children in
# form of 'child_parentId_designation_visibility_extension'
for name, outdata in output.items():
- for filename in glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ):
+ filenames = []
+ if 'new_file_path' in self.app.config.collect_outputs_from:
+ filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ) )
+ if 'job_working_directory' in self.app.config.collect_outputs_from:
+ filenames.extend( glob.glob(os.path.join(job_working_directory,"child_%i_*" % outdata.id) ) )
+ for filename in filenames:
if not name in children:
children[name] = {}
fields = os.path.basename(filename).split("_")
@@ -2213,7 +2218,7 @@
self.sa_session.add( child_dataset )
self.sa_session.flush()
return children
- def collect_primary_datasets( self, output):
+ def collect_primary_datasets( self, output, job_working_directory ):
"""
Find any additional datasets generated by a tool and attach (for
cases where number of outputs is not known in advance).
@@ -2223,7 +2228,12 @@
# datasets in form of:
# 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)'
for name, outdata in output.items():
- for filename in glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ):
+ filenames = []
+ if 'new_file_path' in self.app.config.collect_outputs_from:
+ filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ) )
+ if 'job_working_directory' in self.app.config.collect_outputs_from:
+ filenames.extend( glob.glob(os.path.join(job_working_directory,"primary_%i_*" % outdata.id) ) )
+ for filename in filenames:
if not name in primary_datasets:
primary_datasets[name] = {}
fields = os.path.basename(filename).split("_")
diff -r 99419b4be32d1054c9b58f1664d8f1ab37ac91ac -r 26403ed86d4ccf39ea88c2658012a9a99d453266 universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -151,7 +151,6 @@
# 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
@@ -172,6 +171,14 @@
# Path to the directory containing the external_service_types defined in the config.
#external_service_type_path = external_service_types
+# Tools with a number of outputs not known until runtime can write these
+# outputs to a directory for collection by Galaxy when the job is done.
+# Previously, this directory was new_file_path, but using one global directory
+# can cause performance problems, so using job_working_directory ('.' or cwd
+# when a job is run) is encouraged. By default, both are checked to avoid
+# breaking existing tools.
+#collect_outputs_from = new_file_path,job_working_directory
+
# -- Mail and notification
# Galaxy sends mail for various things: Subscribing users to the mailing list
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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