April 2009 - galaxy-dev - lists.galaxyproject.org

Major updates to Galaxy feature set
by Nate Coraor 15 Apr '09

15 Apr '09

Hi, We've recently been maintaining two separate branches of the Galaxy code base, since significant new features were in progress. Some of you may have already seen these features, namely, dataset security and libraries. All of these changes have now been incorporated in to our main branch. We spared you the 589 change emails that would've been sent, so if you are interested in everything that's changed, see the source at: http://www.bx.psu.edu/hg/galaxy/ Please note that if you update your local instance of Galaxy, significant database changes are required. We've added support for the SQLAlchemy Migrate extension so database upgrades should now be relatively painless, but please back up your database before upgrading. As always, any problems can be discussed here or reported to galaxy-bugs(a)bx.psu.edu. Thanks, --nate

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Tools with multiple output files in galaxy
by svalbard colaco 12 Apr '09

12 Apr '09

Hi all, I had a tool integrated in galaxy storing multiple output files in a folder, Any pointers on how to display these multiple output files in the history panel ? Have got to know how to display for tools giving single onput files as shown in the tutorial. Have also come across some parameter in one of the forum on $outputfiles.files_path , will that help me ? Any pointers in this regard will be of great help. Thanking you'll Regards, sv.

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[hg] galaxy 1746: Re-fix the default test port...
by Greg Von Kuster 09 Apr '09

09 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1c923b889e90 changeset: 1746:1c923b889e90 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Mar 27 16:55:34 2009 -0400 description: Re-fix the default test port... 1 file(s) affected in this change: test/functional/__init__.py diffs (12 lines): diff -r 6c555b0460f1 -r 1c923b889e90 test/functional/__init__.py --- a/test/functional/__init__.py Fri Mar 27 16:37:49 2009 -0400 +++ b/test/functional/__init__.py Fri Mar 27 16:55:34 2009 -0400 @@ -24,7 +24,7 @@ # server (for running the tests against a running instance) default_galaxy_test_host = "localhost" -default_galaxy_test_port = "9879" +default_galaxy_test_port = "9999" default_galaxy_locales = 'en' galaxy_test_file_dir = "test-data" server = None

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[hg] galaxy 1748: Apply i18n fixes from Takashi Hatakeyama and M...
by Greg Von Kuster 09 Apr '09

09 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/09763a5f6ac6 changeset: 1748:09763a5f6ac6 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Apr 09 09:00:58 2009 -0400 description: Apply i18n fixes from Takashi Hatakeyama and Mitsuteru Nakao. 4 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/jobs/__init__.py lib/galaxy/tools/__init__.py lib/galaxy/web/controllers/root.py diffs (51 lines): diff -r e2be1e679ab1 -r 09763a5f6ac6 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Fri Apr 03 13:25:01 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Apr 09 09:00:58 2009 -0400 @@ -121,7 +121,7 @@ line = line.strip() if not line: continue - out.append( '<tr><td>%s</td></tr>' % escape( unicode( line, 'utf-8' ) ) ) + out.append( '<tr><td>%s</td></tr>' % escape( unicode( line ) ) ) out.append( '</table>' ) out = "".join( out ) except Exception, exc: diff -r e2be1e679ab1 -r 09763a5f6ac6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Apr 03 13:25:01 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Apr 09 09:00:58 2009 -0400 @@ -472,7 +472,10 @@ elif dataset.has_data(): # Only set metadata values if they are missing... dataset.set_meta( overwrite = False ) - dataset.set_peek() + if self.tool.is_multi_byte: + dataset.set_multi_byte_peek() + else: + dataset.set_peek() else: dataset.blurb = "empty" dataset.flush() diff -r e2be1e679ab1 -r 09763a5f6ac6 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Fri Apr 03 13:25:01 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Thu Apr 09 09:00:58 2009 -0400 @@ -288,6 +288,8 @@ if not self.version: # For backward compatibility, some tools may not have versions yet. self.version = "1.0.0" + # Support multi-byte tools + self.is_multi_byte = util.string_as_bool( root.get( "is_multi_byte", False ) ) # Type of tool self.tool_type = root.get( "tool_type", None ) # data_source tool diff -r e2be1e679ab1 -r 09763a5f6ac6 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Fri Apr 03 13:25:01 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Apr 09 09:00:58 2009 -0400 @@ -104,7 +104,7 @@ if data.state != state: rval[id] = { "state": data.state, - "html": trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ) + "html": unicode( trans.fill_template( "root/history_item.mako", data=data, hid=data.hid ), 'utf-8' ) } return rval

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[hg] galaxy 1747: Added a new option to specify minimum match va...
by Greg Von Kuster 09 Apr '09

09 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e2be1e679ab1 changeset: 1747:e2be1e679ab1 user: guru date: Fri Apr 03 13:25:01 2009 -0400 description: Added a new option to specify minimum match value in the liftOver tool. 2 file(s) affected in this change: tools/extract/liftOver_wrapper.py tools/extract/liftOver_wrapper.xml diffs (69 lines): diff -r 1c923b889e90 -r e2be1e679ab1 tools/extract/liftOver_wrapper.py --- a/tools/extract/liftOver_wrapper.py Fri Mar 27 16:55:34 2009 -0400 +++ b/tools/extract/liftOver_wrapper.py Fri Apr 03 13:25:01 2009 -0400 @@ -12,20 +12,24 @@ sys.stderr.write(msg) sys.exit() -if len( sys.argv ) != 6: - stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey" ) +if len( sys.argv ) != 7: + stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey minMatch" ) infile = sys.argv[1] outfile1 = sys.argv[2] outfile2 = sys.argv[3] in_dbkey = sys.argv[4] mapfilepath = sys.argv[5] - +minMatch = sys.argv[6] +try: + assert float(minMatch) +except: + minMatch = 0.1 #ensure dbkey is set if in_dbkey == "?": stop_err( "Input dataset genome build unspecified, click the pencil icon in the history item to specify it." ) -cmd_line = "liftOver " + infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + " > /dev/null 2>&1" +cmd_line = "liftOver -minMatch=" + minMatch + " " + infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + " > /dev/null 2>&1" if not os.path.isfile( mapfilepath ): stop_err( "%s mapping is not currently available." % ( mapfilepath.split('/')[-1].split('.')[0] ) ) diff -r 1c923b889e90 -r e2be1e679ab1 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml Fri Mar 27 16:55:34 2009 -0400 +++ b/tools/extract/liftOver_wrapper.xml Fri Apr 03 13:25:01 2009 -0400 @@ -1,11 +1,11 @@ <tool id="liftOver1" name="Convert genome coordinates"> <description> between assemblies and genomes</description> - <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey</command> + <command interpreter="python">liftOver_wrapper.py $input "$out_file1" "$out_file2" $dbkey $to_dbkey $minMatch</command> <inputs> <param format="interval" name="input" type="data" label="Convert coordinates of"> <validator type="unspecified_build" /> <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." /> - </param> + </param> <param name="to_dbkey" type="select" label="To"> <options from_file="liftOver.loc"> <column name="name" index="1"/> @@ -13,7 +13,8 @@ <column name="dbkey" index="0"/> <filter type="data_meta" ref="input" key="dbkey" column="0" /> </options> - </param> + </param> + <param name="minMatch" size="10" type="float" value="0.10" label="Minimum ratio of bases that must remap" /> </inputs> <outputs> <data format="input" name="out_file1" /> @@ -26,7 +27,8 @@ <tests> <test> <param name="input" value="5.bed" dbkey="hg18" ftype="bed" /> - <param name="to_dbkey" value="/depot/data2/galaxy/hg18/liftOver/hg18ToPanTro2.over.chain" /> + <param name="to_dbkey" value="/depot/data2/galaxy/hg18/liftOver/hg18ToPanTro2.over.chain" /> + <param name="misMatch" value="0.95" /> <output name="out_file1" file="5_liftover_mapped.bed"/> <output name="out_file2" file="5_liftover_unmapped.bed"/> </test>

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