1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/8227055957e5/
changeset: 8227055957e5
user: dan
date: 2011-10-20 22:38:14
summary: Update sff extractor to version 0.2.10.
affected #: 2 files (-1 bytes)
--- a/tools/filters/sff_extract.py Thu Oct 20 10:24:19 2011 -0400
+++ b/tools/filters/sff_extract.py Thu Oct 20 16:38:14 2011 -0400
@@ -27,7 +27,7 @@
__author__ = 'Jose Blanca and Bastien Chevreux'
__copyright__ = 'Copyright 2008, Jose Blanca, COMAV, and Bastien Chevreux'
__license__ = 'GPLv3 or later'
-__version__ = '0.2.8'
+__version__ = '0.2.10'
__email__ = 'jblanca(a)btc.upv.es'
__status__ = 'beta'
@@ -298,7 +298,8 @@
#we check that we're removing the asked tag
if tag is not None and tag != last_tag:
- raise RuntimeError("The given xml tag wasn't the last one in the file")
+ etxt=join('The given xml tag (',tag,') was not the last one in the file');
+ raise RuntimeError(etxt)
# while we are at it: also remove all white spaces in that line :-)
i -= 1
@@ -843,7 +844,7 @@
if len(boundaries) == 3:
# case: mask char on both sides of sequence
#print "bounds3"
- data['clip_adapter_left']=1+boundaries[0][1]
+ data['clip_adapter_left']=boundaries[0][1]
data['clip_adapter_right']=boundaries[2][0]
elif len(boundaries) == 2:
# case: mask char left or right of sequence
@@ -851,7 +852,7 @@
if maskedseq[0] == maskchar :
# case: mask char left
#print "left"
- data['clip_adapter_left']=1+boundaries[0][1]
+ data['clip_adapter_left']=boundaries[0][1]
else:
# case: mask char right
#print "right"
@@ -1192,7 +1193,11 @@
'''
left, right = return_merged_clips(data)
seq = data['bases']
- new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower()))
+ if left >= right:
+ new_seq = seq.lower()
+ else:
+ new_seq = ''.join((seq[:left-1].lower(), seq[left-1:right], seq[right:].lower()))
+
return new_seq
def clip_read(data):
@@ -1209,14 +1214,14 @@
-def tests_for_ssaha(linker_fname):
+def tests_for_ssaha():
'''Tests whether SSAHA2 can be successfully called.'''
try:
print "Testing whether SSAHA2 is installed and can be launched ... ",
sys.stdout.flush()
fh = open('/dev/null', 'w')
- retcode = subprocess.call(["ssaha2", "-v"], stdout = fh)
+ retcode = subprocess.call(["ssaha2"], stdout = fh)
fh.close()
print "ok."
except :
@@ -1247,6 +1252,8 @@
'''Launches SSAHA2 on the linker and query file, string SSAHA2 output
into the output filehandle'''
+ tests_for_ssaha()
+
try:
print "Searching linker sequences with SSAHA2 (this may take a while) ... ",
sys.stdout.flush()
--- a/tools/filters/sff_extractor.xml Thu Oct 20 10:24:19 2011 -0400
+++ b/tools/filters/sff_extractor.xml Thu Oct 20 16:38:14 2011 -0400
@@ -1,4 +1,4 @@
-<tool id="Sff_extractor" name="SFF converter" version="1.0.0">
+<tool id="Sff_extractor" name="SFF converter" version="1.0.1"><description></description><command interpreter="python">
#if str($fastq_output) == "fastq_false" #sff_extract.py $clip --seq_file=$out_file3 --qual_file=$out_file4 --xml_file=$out_file2 $input
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/2ed732bca4f6/
changeset: 2ed732bca4f6
user: dan
date: 2011-10-20 16:03:28
summary: Allow toolbox tests to test 0 instances of a repeat.
affected #: 1 file (-1 bytes)
--- a/test/functional/test_toolbox.py Thu Oct 20 09:37:02 2011 -0400
+++ b/test/functional/test_toolbox.py Thu Oct 20 10:03:28 2011 -0400
@@ -59,7 +59,7 @@
# See if we have a grouping.Repeat element
repeat_name = None
for input_name, input_value in testdef.tool.inputs_by_page[0].items():
- if isinstance( input_value, grouping.Repeat ):
+ if isinstance( input_value, grouping.Repeat ) and all_inputs.get( input_name, 1 ) not in [ 0, "0" ]: #default behavior is to test 1 repeat, for backwards compatibility
repeat_name = input_name
break
#check if we need to verify number of outputs created dynamically by tool
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/fcaf6ec8e51b/
changeset: fcaf6ec8e51b
user: greg
date: 2011-10-18 17:41:08
summary: Add new tool attributes to hold information about tools installed from a Galaxy tool shed. Enhance the toolbox's <tool> tag parser to handle these new tool attributes for installed tools. Enhance the Workflow import and load functions to search these new attributes when looking for required tools in the Galaxy instance.
affected #: 2 files (-1 bytes)
--- a/lib/galaxy/tools/__init__.py Tue Oct 18 10:50:16 2011 -0400
+++ b/lib/galaxy/tools/__init__.py Tue Oct 18 11:41:08 2011 -0400
@@ -104,6 +104,14 @@
try:
path = elem.get( "file" )
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid )
+ if guid is not None:
+ # Tool was installed from a Galaxy tool shed.
+ tool.tool_shed = elem.find( "tool_shed" ).text
+ tool.repository_name = elem.find( "repository_name" ).text
+ tool.repository_owner = elem.find( "repository_owner" ).text
+ tool.changeset_revision = elem.find( "changeset_revision" ).text
+ tool.old_id = elem.find( "id" ).text
+ tool.version = elem.find( "version" ).text
if self.app.config.get_bool( 'enable_tool_tags', False ):
tag_names = elem.get( "tags", "" ).split( "," )
for tag_name in tag_names:
@@ -364,9 +372,7 @@
# legacy basic mode - provide compatible defaults
self.attributes['split_size'] = 20
self.attributes['split_mode'] = 'number_of_parts'
-
-
-
+
class Tool:
"""
Represents a computational tool that can be executed through Galaxy.
@@ -387,6 +393,13 @@
# easily ensure that parameter dependencies like index files or
# tool_data_table_conf.xml entries exist.
self.input_params = []
+ # Attributes of tools installed from Galaxy tool sheds.
+ self.tool_shed = None
+ self.repository_name = None
+ self.repository_owner = None
+ self.changeset_revision = None
+ self.old_id = None
+ self.version = None
# Parse XML element containing configuration
self.parse( root, guid=guid )
@@ -407,14 +420,14 @@
raise Exception, "Missing tool 'name'"
# Get the UNIQUE id for the tool
# TODO: can this be generated automatically?
- if guid is not None:
+ if guid is None:
+ self.id = root.get( "id" )
+ self.version = root.get( "version" )
+ else:
self.id = guid
- else:
- self.id = root.get( "id" )
if not self.id:
- raise Exception, "Missing tool 'id'"
- self.version = root.get( "version" )
- if not self.version:
+ raise Exception, "Missing tool 'id'"
+ if not self.version:
# For backward compatibility, some tools may not have versions yet.
self.version = "1.0.0"
# Support multi-byte tools
--- a/lib/galaxy/workflow/modules.py Tue Oct 18 10:50:16 2011 -0400
+++ b/lib/galaxy/workflow/modules.py Tue Oct 18 11:41:08 2011 -0400
@@ -171,15 +171,10 @@
except KeyError, e:
# Handle the case where the workflow requires a tool not available in the local Galaxy instance.
self.tool = None
- # TODO: Instead of parsing the guid, get the tool_id and version from the shed_tool_conf.xml,
- # which requires enhancements to the tool loading process.
+ # The id value of tools installed from a Galaxy tool shed is a guid, but
+ # these tool's old_id attribute should contain what we're looking for.
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.
+ if tool_id == available_tool.old_id:
self.tool = available_tool
break
self.post_job_actions = {}
@@ -211,13 +206,10 @@
tool_id = step.tool_id
install_tool_id = None
if tool_id not in trans.app.toolbox.tools_by_id:
+ # The id value of tools installed from a Galaxy tool shed is a guid, but
+ # these tool's old_id attribute should contain what we're looking for.
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.
+ if tool_id == available_tool.old_id:
install_tool_id = available_tool_id
break
if tool_id in trans.app.toolbox.tools_by_id or install_tool_id:
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