Hi Greg & Nate,

Thanks for your comments. I had changed the port and tried to run the test again, but it fails in an AssertionError
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mGenePredict ( mgenepredict ) > Test-1 ... FAIL

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FAIL: mGenePredict ( mgenepredict ) > Test-1
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Traceback (most recent call last):
File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 114, in test_tool
    self.do_it()
File "/home/galaxy/galaxy-2.1.2009/test/functional/test_toolbox.py", line 54, in do_it
    self.verify_dataset_correctness( file )
File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 323, in verify_dataset_correctness
    if wait: self.wait() #wait for job to finish
File "/home/galaxy/galaxy-2.1.2009/test/base/twilltestcase.py", line 617, in wait
    self.assertNotEqual(count, maxiter)
AssertionError: 20 == 20

-------------------- >> begin captured stdout << ---------------------
galaxy.tools.actions.upload INFO 2009-10-23 10:15:59,551 tool upload1 created job id 1
galaxy.tools.actions.upload INFO 2009-10-23 10:15:59,897 job id 1 ended ok, file size: 390.6 Kb
Uploaded file: tair9_chr4_10000.fas , ftype: fasta , extra: {'ftype': 'fasta', 'value': 'tair9_chr4_10000.fas'}

form 'tool_form' contains the following controls ( note the values )
control 0: <HiddenControl(tool_id=mgenepredict) (readonly)>
control 1: <HiddenControl(tool_state=800254e3010000306361383263373039613935626566386164663739383835643632653966356537376437656533393a3762323236383639373337343666373237393566373637333566373037323635373437323631363936653635363432323361323032323762356332323733366637353732363336353563323233613230356332323730373236353734373236313639366536353634356332323263323035633232366637323637363136653639373336643563323233613230356332323635366336353637363136653733356332323263323035633232356635663633373537323732363536653734356636333631373336353566356635633232336132303330376432323263323032323566356637303631363736353566356632323361323033303263323032323638363937333734366637323739356637363733356636393665373436353732366536313663323233613230323237623563323237333666373537323633363535633232336132303563323236383639373337343666373237393563323232633230356332323636363137333734363135663639366537303735373435633232336132303331326332303563323235663566363337353732373236353665373435663633363137333635356635663563323233613230333037643232376471002e) (readonly)>
control 2: <SubmitControl(runtool_btn=Execute) (readonly)>
control 3: <SelectControl(history_vs_internal|source=[*history, internal])>
base.twilltestcase DEBUG 2009-10-23 10:15:59,975 In submit_form, continuing, but caught exception: 'history_vs_internal|source'
control 4: <SelectControl(history_vs_internal|fasta_input=[*1])>
control 5: <SelectControl(history_vs_pretrained|source=[*pretrained, history])>
control 6: <SelectControl(history_vs_pretrained|organism=[*elegans, arabidopsis])>
control 7: <SubmitControl(runtool_btn=Execute) (readonly)>
page_inputs (0) {'history_vs_pretrained|source': ['pretrained'], 'history_vs_pretrained|organism': ['arabidopsis']}
galaxy.jobs DEBUG 2009-10-23 10:16:05,321 dispatching job 2 to local runner
galaxy.jobs DEBUG 2009-10-23 10:16:05,502 job 2 dispatched
galaxy.jobs.runners.local DEBUG 2009-10-23 10:16:05,770 executing: ~/bin/octave_start_script.sh "setup_mgene; galaxy_mgene_predict(     '/tmp/tmpTpQQ6I/database/files/000/dataset_1.dat', '/tmp/tmpTpQQ6I/database/files/000/dataset_1_files',      '', 'mgene:arabidopsis',      '/tmp/tmpTpQQ6I/database/files/000/dataset_3.dat', '/tmp/tmpTpQQ6I/database/files/000/dataset_3_files', -1);">> /tmp/tmpTpQQ6I/database/files/000/dataset_2.dat ; ~/bin/cleanup_output.sh /tmp/tmpTpQQ6I/database/files/000/dataset_2.dat

--------------------- >> end captured stdout << ----------------------
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Ran 1 test in 227.029s
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Many thanks in advance,
Vipin T S