- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 3501: Add a helper script that will re.escape files; ...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e4592fc99acc changeset: 3501:e4592fc99acc user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Mar 09 15:25:23 2010 -0500 description: Add a helper script that will re.escape files; useful for creating files valid for re_match and re_match_multiline comparisons in tool tests. diffstat: scripts/tools/re_escape_output.py | 34 ++++++++++++++++++++++++++++++++++ 1 files changed, 34 insertions(+), 0 deletions(-) diffs (38 lines): diff -r c67b5628f348 -r e4592fc99acc scripts/tools/re_escape_output.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/tools/re_escape_output.py Tue Mar 09 15:25:23 2010 -0500 @@ -0,0 +1,34 @@ +#! /usr/bin/python + +""" +Escapes a file into a form suitable for use with tool tests using re_match or re_match_multiline (when -m/--multiline option is used) + +usage: re_escape_output.py [options] input_file [output_file] + -m: Use Multiline Matching +""" + +import optparse, re + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( "-m", "--multiline", action="store_true", dest="multiline", default=False, help="Use Multiline Matching") + ( options, args ) = parser.parse_args() + input = open( args[0] ,'rb' ) + if len( args ) > 1: + output = open( args[1], 'wb' ) + else: + if options.multiline: + suffix = 're_match_multiline' + else: + suffix = 're_match' + output = open( "%s.%s" % ( args[0], suffix ), 'wb' ) + if options.multiline: + lines = [ re.escape( input.read() ) ] + else: + lines = [ "%s\n" % re.escape( line.rstrip( '\n\r' ) ) for line in input ] + output.writelines( lines ) + output.close() + +if __name__ == "__main__": + __main__()

1 0

[hg] galaxy 3500: Add server_side_cursors to database_engine_opt...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c67b5628f348 changeset: 3500:c67b5628f348 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 09 14:51:01 2010 -0500 description: Add server_side_cursors to database_engine_option_ parsing diffstat: lib/galaxy/config.py | 3 ++- 1 files changed, 2 insertions(+), 1 deletions(-) diffs (13 lines): diff -r 478447ba0ec6 -r c67b5628f348 lib/galaxy/config.py --- a/lib/galaxy/config.py Tue Mar 09 14:29:17 2010 -0500 +++ b/lib/galaxy/config.py Tue Mar 09 14:51:01 2010 -0500 @@ -172,7 +172,8 @@ 'pool_recycle': int, 'pool_size': int, 'max_overflow': int, - 'pool_threadlocal': string_as_bool + 'pool_threadlocal': string_as_bool, + 'server_side_cursors': string_as_bool } prefix = "database_engine_option_" prefix_len = len( prefix )

1 0

[hg] galaxy 3499: Update tool tests for MAF to interval tool
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/478447ba0ec6 changeset: 3499:478447ba0ec6 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Mar 09 14:29:17 2010 -0500 description: Update tool tests for MAF to interval tool diffstat: tools/maf/maf_to_interval.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 821b6cbbee1c -r 478447ba0ec6 tools/maf/maf_to_interval.xml --- a/tools/maf/maf_to_interval.xml Tue Mar 09 14:28:33 2010 -0500 +++ b/tools/maf/maf_to_interval.xml Tue Mar 09 14:29:17 2010 -0500 @@ -27,7 +27,7 @@ <param name="complete_blocks" value="partial_disallowed"/> <param name="remove_gaps" value="keep_gaps"/> <param name="species" value="panTro1" /> -  + <output name="out_file1" file="maf_to_interval_out_hg17.interval"/> <output name="out_file1" file="maf_to_interval_out_panTro1.interval"/> </test> </tests>

1 0

[hg] galaxy 3498: Allow better testing of tool outputs with an u...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/821b6cbbee1c changeset: 3498:821b6cbbee1c user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Mar 09 14:28:33 2010 -0500 description: Allow better testing of tool outputs with an unknown number of dynamically created outputs. diffstat: test/functional/test_toolbox.py | 11 ++++++++++- 1 files changed, 10 insertions(+), 1 deletions(-) diffs (28 lines): diff -r a719c6971613 -r 821b6cbbee1c test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Tue Mar 09 14:13:05 2010 -0500 +++ b/test/functional/test_toolbox.py Tue Mar 09 14:28:33 2010 -0500 @@ -53,6 +53,11 @@ if isinstance( input_value, grouping.Repeat ): repeat_name = input_name break + #check if we need to verify number of outputs created dynamically by tool + if testdef.tool.force_history_refresh: + job_finish_by_output_count = len( self.get_history_as_data_list() ) + else: + job_finish_by_output_count = False # Do the first page page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs) # Run the tool @@ -65,7 +70,11 @@ print "page_inputs (%i)" % i, page_inputs # Check the results ( handles single or multiple tool outputs ). Make sure to pass the correct hid. # The output datasets from the tool should be in the same order as the testdef.outputs. - data_list = self.get_history_as_data_list() + data_list = None + while data_list is None: + data_list = self.get_history_as_data_list() + if job_finish_by_output_count and len( testdef.outputs ) > ( len( data_list ) - job_finish_by_output_count ): + data_list = None self.assertTrue( data_list ) elem_index = 0 - len( testdef.outputs ) for output_tuple in testdef.outputs:

1 0

[hg] galaxy 3497: Update psycopg2 to 2.0.13/postgresql 8.4.2
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a719c6971613 changeset: 3497:a719c6971613 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Mar 09 14:13:05 2010 -0500 description: Update psycopg2 to 2.0.13/postgresql 8.4.2 diffstat: dist-eggs.ini | 2 +- eggs.ini | 6 +- scripts/scramble/scripts/psycopg2-linux.py | 1 + scripts/scramble/scripts/psycopg2-macosx.py | 85 ++++++++++++++++++++++++++++ scripts/scramble/scripts/psycopg2-solaris.py | 1 + scripts/scramble/scripts/psycopg2.py | 1 + 6 files changed, 92 insertions(+), 4 deletions(-) diffs (162 lines): diff -r 5f7ace3195b7 -r a719c6971613 dist-eggs.ini --- a/dist-eggs.ini Tue Mar 09 13:54:30 2010 -0500 +++ b/dist-eggs.ini Tue Mar 09 14:13:05 2010 -0500 @@ -22,7 +22,7 @@ py2.4-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.4 py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5 py2.6-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.6 -py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6 +py2.6-macosx-10.6-universal-ucs2 = bach.bx.psu.edu /usr/bin/python2.6 py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4 py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5 py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6 diff -r 5f7ace3195b7 -r a719c6971613 eggs.ini --- a/eggs.ini Tue Mar 09 13:54:30 2010 -0500 +++ b/eggs.ini Tue Mar 09 14:13:05 2010 -0500 @@ -17,7 +17,7 @@ DRMAA_python = 0.2 MySQL_python = 1.2.3c1 pbs_python = 2.9.4 -psycopg2 = 2.0.6 +psycopg2 = 2.0.13 pycrypto = 2.0.1 pysam = 0.1.1 pysqlite = 2.5.6 @@ -56,7 +56,7 @@ ; extra version information [tags] -psycopg2 = _8.2.6_static +psycopg2 = _8.4.2_static pysqlite = _3.6.17_static MySQL_python = _5.1.41_static bx_python = _dev_3b9d30e47619 @@ -68,5 +68,5 @@ ; the wiki page above [source] MySQL_python = mysql-5.1.41 -psycopg2 = postgresql-8.2.6 +psycopg2 = postgresql-8.4.2 pysqlite = sqlite-amalgamation-3_6_17 diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2-linux.py --- a/scripts/scramble/scripts/psycopg2-linux.py Tue Mar 09 13:54:30 2010 -0500 +++ b/scripts/scramble/scripts/psycopg2-linux.py Tue Mar 09 14:13:05 2010 -0500 @@ -20,6 +20,7 @@ "Configuring postgres (./configure)" ) # compile + run( "make ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; make ../../src/include/utils/fmgroids.h)" ) run( "make", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" ) run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" ) diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2-macosx.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/psycopg2-macosx.py Tue Mar 09 14:13:05 2010 -0500 @@ -0,0 +1,85 @@ +import os, sys, shutil +from distutils.sysconfig import get_config_var + +def prep_postgres( prepped, args ): + + pg_version = args['version'] + pg_srcdir = os.path.join( os.getcwd(), "postgresql-%s" % pg_version ) + + # set up environment + os.environ['CC'] = get_config_var('CC') + os.environ['CFLAGS'] = get_config_var('CFLAGS') + os.environ['LDFLAGS'] = get_config_var('LDFLAGS') + + if '-fPIC' not in os.environ['CFLAGS']: + os.environ['CFLAGS'] += ' -fPIC' + + # run configure + run( "./configure --prefix=%s/postgres --disable-dependency-tracking --enable-static --disable-shared --without-readline --with-thread-safety" % os.getcwd(), + os.path.join( os.getcwd(), "postgresql-%s" % pg_version ), + "Configuring postgres (./configure)" ) + + # compile + run( "make ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; make ../../src/include/utils/fmgroids.h)" ) + run( "make all-static-lib", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" ) + run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" ) + + # install + run( "make install-lib-static", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make install)" ) + run( "make install", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make install)" ) + run( "make install", os.path.join( pg_srcdir, 'src', 'include' ), "Compiling pg_config (cd src/include; make install)" ) + + # manually install some headers + run( "cp libpq-fe.h %s" % os.path.join( os.getcwd(), 'postgres', 'include' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" ) + run( "cp libpq-events.h %s" % os.path.join( os.getcwd(), 'postgres', 'include' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" ) + run( "cp libpq-int.h %s" % os.path.join( os.getcwd(), 'postgres', 'include', 'internal' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" ) + run( "cp pqexpbuffer.h %s" % os.path.join( os.getcwd(), 'postgres', 'include', 'internal' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" ) + + # create prepped archive + print "%s(): Creating prepped archive for future builds at:" % sys._getframe().f_code.co_name + print " ", prepped + compress( prepped, + 'postgres/bin', + 'postgres/include', + 'postgres/lib' ) + +if __name__ == '__main__': + + # change back to the build dir + if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + + # find setuptools + sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) ) + from scramble_lib import * + + tag = get_tag() + + pg_version = ( tag.split( "_" ) )[1] + pg_archive_base = os.path.join( archives, "postgresql-%s" % pg_version ) + pg_archive = get_archive( pg_archive_base ) + pg_archive_prepped = os.path.join( archives, "postgresql-%s-%s.tar.gz" % ( pg_version, platform_noucs ) ) + + # clean up any existing stuff (could happen if you run scramble.py by hand) + clean( [ 'postgresql-%s' % pg_version ] ) + + # unpack postgres + unpack_dep( pg_archive, pg_archive_prepped, prep_postgres, dict( version=pg_version ) ) + + # localize setup.cfg + if not os.path.exists( 'setup.cfg.orig' ): + shutil.copy( 'setup.cfg', 'setup.cfg.orig' ) + f = open( 'setup.cfg', 'a' ) + f.write( '\npg_config=postgres/bin/pg_config\n' ) + f.close() + + # tag + me = sys.argv[0] + sys.argv = [ me ] + if tag is not None: + sys.argv.append( "egg_info" ) + sys.argv.append( "--tag-build=%s" %tag ) + sys.argv.append( "bdist_egg" ) + + # go + execfile( "setup.py", globals(), locals() ) diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2-solaris.py --- a/scripts/scramble/scripts/psycopg2-solaris.py Tue Mar 09 13:54:30 2010 -0500 +++ b/scripts/scramble/scripts/psycopg2-solaris.py Tue Mar 09 14:13:05 2010 -0500 @@ -23,6 +23,7 @@ "Configuring postgres (./configure)" ) # compile + run( "gmake ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; gmake ../../src/include/utils/fmgroids.h)" ) run( "gmake", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; gmake)" ) run( "gmake", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; gmake)" ) diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2.py --- a/scripts/scramble/scripts/psycopg2.py Tue Mar 09 13:54:30 2010 -0500 +++ b/scripts/scramble/scripts/psycopg2.py Tue Mar 09 14:13:05 2010 -0500 @@ -20,6 +20,7 @@ "Configuring postgres (./configure)" ) # compile + run( "make ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; make ../../src/include/utils/fmgroids.h)" ) run( "make", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" ) run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" )

1 0

[hg] galaxy 3496: Allow uploading and use of composite files in ...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5f7ace3195b7 changeset: 3496:5f7ace3195b7 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Tue Mar 09 13:54:30 2010 -0500 description: Allow uploading and use of composite files in toolbox tests. Along with setting each component of a composite datatype, metadata attributes (e.g. basename in Rgenetics datatypes) can be set. Example Tool: <tool id='temp' name='temp test'> <description>test</description> <command>cat ${i.extra_files_path}/${i.metadata.base_name}.fam > $out_file1</command> <inputs> <param name="i" type="data" label="RGenetics genotype data from your current history" format="pbed" /> </inputs> <outputs> <data format="text" name="out_file1" /> </outputs> <tests> <test> <param name='i' ftype='pbed'> <metadata name='base_name' value='rgenetics_CHANGED' /> <composite_data value='temp/somefile1' /> <composite_data value='temp/somefile2' /> <composite_data value='temp/somefile3' /> </param> <output name='out_file1' file='temp/somefile3' /> </test> </tests> </tool> diffstat: lib/galaxy/tools/__init__.py | 1 + lib/galaxy/tools/test.py | 4 +++- test/base/twilltestcase.py | 16 ++++++++++++---- test/functional/test_toolbox.py | 5 ++++- 4 files changed, 20 insertions(+), 6 deletions(-) diffs (73 lines): diff -r 3b1be99d1f62 -r 5f7ace3195b7 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Mar 09 11:28:21 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Tue Mar 09 13:54:30 2010 -0500 @@ -523,6 +523,7 @@ value = attrib['value'] else: value = None + attrib['children'] = list( param_elem.getchildren() ) test.add_param( attrib.pop( 'name' ), value, attrib ) for output_elem in test_elem.findall( "output" ): attrib = dict( output_elem.attrib ) diff -r 3b1be99d1f62 -r 5f7ace3195b7 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Tue Mar 09 11:28:21 2010 -0500 +++ b/lib/galaxy/tools/test.py Tue Mar 09 13:54:30 2010 -0500 @@ -30,10 +30,12 @@ if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None: + if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) == 0: assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name else: self.required_files.append( ( value, extra ) ) + if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) > 0: + value = extra.get( 'ftype' ) except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) diff -r 3b1be99d1f62 -r 5f7ace3195b7 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Mar 09 11:28:21 2010 -0500 +++ b/test/base/twilltestcase.py Tue Mar 09 13:54:30 2010 -0500 @@ -142,14 +142,22 @@ filename = os.path.join( *path ) file(filename, 'wt').write(buffer.getvalue()) - def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)' ): + def upload_file( self, filename, ftype='auto', dbkey='unspecified (?)', metadata = None, composite_data = None ): """Uploads a file""" - filename = self.get_filename(filename) self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: - tc.fv("1","file_type", ftype) + self.refresh_form( "file_type", ftype ) #Refresh, to support composite files tc.fv("1","dbkey", dbkey) - tc.formfile("1","file_data", filename) + if metadata: + for elem in metadata: + tc.fv( "1", "files_metadata|%s" % elem.get( 'name' ), elem.get( 'value' ) ) + if composite_data: + for i, composite_file in enumerate( composite_data ): + filename = self.get_filename( composite_file.get( 'value' ) ) + tc.formfile( "1", "files_%i|file_data" % i, filename ) + else: + filename = self.get_filename( filename ) + tc.formfile( "1", "file_data", filename ) tc.submit("runtool_btn") self.home() except AssertionError, err: diff -r 3b1be99d1f62 -r 5f7ace3195b7 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Tue Mar 09 11:28:21 2010 -0500 +++ b/test/functional/test_toolbox.py Tue Mar 09 13:54:30 2010 -0500 @@ -32,7 +32,10 @@ raise AssertionError("ToolTestCase.do_it failed") # Upload any needed files for fname, extra in testdef.required_files: - self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ) ) + children = extra.get( 'children', [] ) + metadata = [ child for child in children if child.tag == 'metadata' ] + composite_data = [ child for child in children if child.tag == 'composite_data' ] + self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ), metadata = metadata, composite_data = composite_data ) print "Uploaded file: ", fname, ", ftype: ", extra.get( 'ftype', 'auto' ), ", extra: ", extra # We need to handle the case where we've uploaded a valid compressed file since the upload # tool will have uncompressed it on the fly.

1 0

mysql setup / upload speed for fastq
by Nathaniel Street 11 Mar '10

11 Mar '10

Hi I have set galaxy to use mysql on localhost but I could not workout the syntax for the database_connection line to specify a username and password. Is this possible? I'm using Ubuntu so as per the install guide I have this database_connection = mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock I wanted to try mysql to see if it was faster for uploads of very large NGS files. At the moment even uploading a file from the localhost is very very slow. Is this normal or are there some ways to speed it up? My fastq files are all > 10GB. Maybe using Galaxy isn't the right way to go and I should use the tools locally but as NGS handling is in there I am guessing large files were in mind? Thanks Nathaniel -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org

2 2

Adding custom genome
by Nathaniel Street 11 Mar '10

11 Mar '10

Hi I'm trying to add a custom genome to a local galaxy install. So far I have done this: 1)Create a fasta file per scaffold (it's an unfinished genome) 2)Create a nib file per one of those scaffold fasta files 3)Add an entry to build.txt nis Test genome (nis) 4)Add a line to alignseq.loc seq nis /data/nib/nis 5)Add a line to faseq.loc nis /data/sequences/nis Is there more that I need to do to be able to extract sequences using the Extract Genomic DNA tool? I tried to use the tool by uploading a GFF3 file, extracting a small part of that for testing and then using that small part to extract genomic DNA. When I try this I get an error message returned AttributeError: 'tuple' object has no attribute 'iteritems' And the text version of the Traceback gives this URL: http://XXX:XXX:XX:XX:8080/tool_runner/index File '/home/nat/work/software/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/nat/work/software/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/nat/work/software/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 53 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 807 in handle_input _, out_data = self.execute( trans, incoming=params ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 1079 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 140 in execute inp_data = self.collect_input_datasets( tool, incoming, trans ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 101 in collect_input_datasets tool.visit_inputs( param_values, visitor ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/__init__.py', line 754 in visit_inputs callback( "", input, value[input.name] ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 85 in visitor input_datasets[ prefix + input.name ] = process_dataset( value ) File '/home/nat/work/software/galaxy-dist/lib/galaxy/tools/actions/__init__.py', line 47 in process_dataset new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] File '/home/nat/work/software/galaxy-dist/lib/galaxy/datatypes/data.py', line 264 in convert_dataset for name, value in converted_dataset.iteritems(): AttributeError: 'tuple' object has no attribute 'iteritems' Can anyone tell me what I'm doing wrong? Do I need more than only the nib files? Many thanks Nathaniel -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org -- Nathaniel Street Umeå Plant Science Centre Department of Plant Physiology University of Umeå SE-901 87 Umeå SWEDEN email: nathaniel.street(a)plantphys.umu.se tel: +46-90-786 5473 fax: +46-90-786 6676 www.popgenie.org

1 0

displaying R output
by Jeremy Goecks 11 Mar '10

11 Mar '10

Hi Zaky, There are people on the galaxy-dev list (cc'd) that will be better able to assist you with this problem than me. Best, J. On Mar 8, 2010, at 12:11 PM, ZAKY ADAM wrote: > Hi Jeremy, > > I am running a perl program that embeds some R commands. The R commands require > a package called "qvalue". Running the R commands included in this package > results in some graphics in PDF. The program works perfectly on my computer, > but does not work on my galaxy that I have on scofield. I need this to run on > scofield in order to complete my workflow. > > The R commands are the following: > > library(tcltk); > library(qvalue); > p <- scan("p_valuesInputFile.txt"); > qobj <- qvalue(p, fdr.level = 0.05); > > I am reading simply 104 p values (in statistics) and save them in the variable > p, then the last command from the "qvalue" package should convert them into > what is called q values, but requires a graphical device. This last line > generates always the following error message: > > Loading Tcl/Tk interface ... done > Warning message: > In fun(...) : no DISPLAY variable so TK is not available > Read 104 items > > You don't need to be concerned with the code itself because, as I said, it > works perfectly on my mac os x computer. The problem is that Galaxy can not > deal with this graphical issue. > I hope that you can be helpful on this. > > Zaky Adam > Postdoctoral Research Fellow > Center for Comparative Genomics and Bioinformatics > The Pennsylvania State University > 306 Wartik Lab > University Park, PA 16802 > (814) 863-2185 > zua4(a)psu.edu >

3 2

Error in parsing XML help
by Chris Cole 10 Mar '10

10 Mar '10

Hi, Me again. I don't know why I've suddenly got all these errors. Updates aren't normally this problematic. This time I've got a huge amount of these errors in my paster.log: galaxy.tools ERROR 2010-03-09 14:12:46,128 error in help for tool Upload File Traceback (most recent call last): File "/homes/www-galaxy/galaxy_live/lib/galaxy/tools/__init__.py", line 489, in parse_help self.help = util.rst_to_html(self.help.text) File "/homes/www-galaxy/galaxy_live/lib/galaxy/util/__init__.py", line 232, in rst_to_html return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) ) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 397, in publish_string enable_exit_status=enable_exit_status) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 607, in publish_programmatically pub.set_components(reader_name, parser_name, writer_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 92, in set_components self.set_reader(reader_name, self.parser, parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/core.py", line 82, in set_reader self.reader = reader_class(parser, parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 51, in __init__ self.set_parser(parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/readers/__init__.py", line 62, in set_parser parser_class = parsers.get_parser_class(parser_name) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/__init__.py", line 48, in get_parser_class module = __import__(parser_name, globals(), locals()) File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/__init__.py", line 77, in <module> from docutils.parsers.rst import states File "/homes/www-galaxy/galaxy_live/eggs/docutils-0.4-py2.6.egg/docutils/parsers/rst/states.py", line 110, in <module> import roman ImportError: No module named roman As far as I can see there's an error (like above) for every tool and the help text for the tools is no longer displayed within Galaxy. Has something changed in how the XML files should be formatted or is it something in the egg that's not right? Thanks again for any help. Cheers, Chris

2 2