[Chinook] Re: Client_Log
Stephen Montgomery
smontgom at bcgsc.bc.ca
Wed Dec 15 08:13:16 PST 2004
Hi Vadim -
I think the reason why services are displayed when you start the client
is that
you won't see anything if the executables/utilities cannot be found.
So the server is advertising nothing, that is why nothing appears in the
client window.
Everything is running smoothly though from the logs.
You just have to change the path of one of your services so that it
points to a valid executable/utility.
i.e. contig_merger in the applications.xml file should have its <path>
point to where it is installed.
Then you should see it. I'm guessing contig_merger isn't in opt/ as below.
Also, it doesn't matter, but you do not need to run the rmiregistry
command as the server will autostart the rmiregistry if one can't be
found (when operating in rmi mode)
All the best,
Stephen
PS. I'm putting our thread on the chinook list so that there is a
permanent record of problems we find. Maybe as well there is some
interest on it for the SSL work we are thinking about (for private
Chinook services). Cheers!
astakhov wrote:
O'k.
This is what I am trying to do.
ant p2p-start
the I start RMI-registry, then from JBuilder (On Windows), I run
ChinookServer
my VM parameters:
-Djava.rmi.server.codebase="file:///C:/Peer2Peer/chinook/classes/
file:///C:/Peer2Peer/chinook/lib/filewire.jar"
-Djava.security.policy="file:///C:/Peer2Peer/chinook/resources/chinookRMI.policy"
Then "ant client"
But it does not write anything in the log file.
log4j:ERROR Could not find value for key log4j.appender.A1
log4j:ERROR Could not instantiate appender named "A1".
log4j:WARN No appenders could be found for logger
(ca.bcgsc.chinook.server.manager.ServerManager).
log4j:WARN Please initialize the log4j system properly.
Probably, I did not set it proparly. But then I have
Chinook Server can be shutdown on port: 7337
2004-12-14 15:56:32,546 [main] INFO
ca.bcgsc.filewire.server.remote.impl.FileWireRealImpl - FileWireRealImpl
instantiated
2004-12-14 15:56:32,546 [main] WARN
ca.bcgsc.filewire.server.remote.impl.FileWireImpl -
java.rmi.server.ServerNotActiveException: not in a remote call
2004-12-14 15:56:32,546 [main] INFO
ca.bcgsc.filewire.server.configuration.Configuration - Reading filewire
configuration file
2004-12-14 15:56:32,562 [main] INFO
ca.bcgsc.filewire.server.remote.impl.FileWireImpl - Attempting to bind
to rmiregistry at: //localhost:1099/FileWireImpl
2004-12-14 15:56:32,671 [main] INFO
ca.bcgsc.filewire.server.remote.impl.FileWireImpl - FileWireImpl bound
2004-12-14 15:56:32,671 [main] INFO
ca.bcgsc.chinook.server.manager.ServerManager - Notify that server started
2004-12-14 15:57:52,250 [RMI TCP Connection(2)-132.239.132.190] INFO
ca.bcgsc.chinook.server.remote.impl.ApplicationServerRealImpl -
ApplicationServerRealImpl: getApplicationTypes()
It looks like, that server started and bound. But I still don't see it
in the client window???
Vadim.
Stephen Montgomery wrote:
> This error message is because you static-services.xml file has a local
> entry which cannot be found. However to get the p2p server running,
> what you did was right
> ant p2p-node
> then wait a few seconds
> then ant-server
> then ant-client
> Should work.
> It doesn't seem that your RMI server is starting correctly though.
> Can you clean the log files (rm chinook.log*) and just run ant server
> and send me the chinook.log for that.
> Can you also send me your application.xml file I will be able to
> debug with those. Cheers,
> Stephen
>
------------------------------------------------------------------------
<chinook>
<version>1.0</version>
<date>2003-07-01 12:00:00 PST</date>
<naming_service_machine>localhost</naming_service_machine>
<naming_service_port>1099</naming_service_port>
<!-- WEBSERVICES
<protocol>WSDL</protocol>
<uri>http://localhost:8080/axis/services/ApplicationServerImpl</uri>
<using_filewire>true</using_filewire>
<filewire_uri>http://localhost:8080/axis/services/FileWireImpl</filewire_uri>
-->
<!-- RMI -->
<protocol>RMI</protocol>
<uri>//localhost:1099/ApplicationServerImpl</uri>
<using_filewire>true</using_filewire>
<filewire_uri>//localhost:1099/FileWireImpl</filewire_uri>
<!-- -->
<preview_size_in_lines>25</preview_size_in_lines>
<publisher>
<name>Stephen Montgomery</name>
<email>smontgom at bcgsc.bc.ca</email>
<documentation_uri>http://smweb.bcgsc.bc.ca</documentation_uri>
</publisher>
<!-- ******************** LAGAN APPLICATION BLOCK ********************* -->
<application>
<name>LAGAN</name>
<type>ALIGNMENT</type>
<path>/opt/mlagan</path>
<executable>lagan.pl</executable>
<format>exe_path/executable dna_sequence parameter</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>true</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.alignment.Lagan</parsing_class>
<output_path>/tmp</output_path>
<description>Lagan is developed at Stanford by Mike Brudno</description>
<creator>http://lagan.stanford.edu</creator>
<version>1</version>
<data_entry_set>
<name>dna_sequence</name>
<maximum_count>2</maximum_count>
<minimum_count>2</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>chaos_STRING</descriptor>
<regex_format>["]([.]+)["]</regex_format>
<description>The contents of this string will be passed as arguments to chaos</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>order_STRING</descriptor>
<regex_format>"-gs ([0-9]+) -gc ([0-9]+) -mt ([0-9]+) -ms ([0-9]+)"</regex_format>
<description>The contents of this string will be passed as arguments to order</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>recurfl_STRING</descriptor>
<regex_format>"(\([0-9]+,[0-9]+,[0-9]+,[0-9]+\),)+"</regex_format>
<description>Used in recursive anchoring</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>translate_BOOLEAN</descriptor>
<description>Use translated anchoring</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>bin_BOOLEAN</descriptor>
<description>Output in binary format</description>
<user_defined>false</user_defined>
<on>false</on>
</parameter>
<parameter>
<descriptor>mfa_BOOLEAN</descriptor>
<description>Output in multifasta format</description>
<user_defined>false</user_defined>
<on>true</on>
</parameter>
<parameter>
<descriptor>rc_BOOLEAN</descriptor>
<description>Reverse complement the second sequence before alignment</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>fastreject_BOOLEAN</descriptor>
<description>Abandon alignment if homology looks weak</description>
<user_defined>true</user_defined>
</parameter>
</application>
<!-- ******************** MLAGAN APPLICATION BLOCK ********************* -->
<application>
<name>MLAGAN</name>
<type>ALIGNMENT</type>
<path>/opt/mlagan</path>
<executable>mlagan</executable>
<format>exe_path/executable dna_sequence parameter -out outputfile1</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>false</results_written_to_stdout>
<output_file>
<match_name>outputfile1</match_name>
<description>Alignment results</description>
</output_file>
<parsing_class>ca.bcgsc.chinook.server.runner.alignment.Lagan</parsing_class>
<output_path>/tmp</output_path>
<description>Lagan is developed at Stanford by Mike Brudno</description>
<creator>http://lagan.stanford.edu</creator>
<version>1</version>
<data_entry_set>
<name>dna_sequence</name>
<minimum_count>2</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>tree_STRING</descriptor>
<regex_format>["]([*]+)["]</regex_format>
<description>This is of the form "(Homo_sapiens Mus_musculus) Danio_rerio)" for your input sequences</description>
<user_defined>true</user_defined>
<use_equals>false</use_equals>
</parameter>
<parameter>
<descriptor>translate_BOOLEAN</descriptor>
<description>Use translated anchoring</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>nested_BOOLEAN</descriptor>
<description>Runs iterative improvement in a nested fashion</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>postir_BOOLEAN</descriptor>
<description>Runs iterative improvement on final alignment</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>fastreject_BOOLEAN</descriptor>
<description>Abandon alignment if homology looks weak</description>
<user_defined>true</user_defined>
</parameter>
</application>
<!-- ******************** CLUSTALW APPLICATION BLOCK ********************* -->
<application>
<name>CLUSTALW</name>
<type>ALIGNMENT</type>
<path>/opt/clustalw/clustalw1.83</path>
<executable>clustalw</executable>
<format>exe_path/executable dna_sequence parameter -outfile=outputfile1</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>false</results_written_to_stdout>
<output_file>
<match_name>outputfile1</match_name>
<description>Alignment results</description>
</output_file>
<parsing_class>ca.bcgsc.chinook.server.runner.alignment.Clustalw</parsing_class>
<output_path>/tmp</output_path>
<description>Clustalw is developed by Thompson, Higgins and Gibson (EMBL)</description>
<creator>http://www.ebi.ac.uk/clustalw/</creator>
<version>1</version>
<data_entry_set>
<name>dna_sequence</name>
<minimum_count>2</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.FastaToMultiFastaOutputter</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>ktup_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Word Size (Pairwise Alignment Param)</description>
<use_equals>true</use_equals>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>topdiags_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Number of Best Diagonals (Pairwise Alignment Param)</description>
<use_equals>true</use_equals>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>window_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Window around Best Diagonals (Pairwise Alignment Param)</description>
<user_defined>true</user_defined>
<use_equals>true</use_equals>
</parameter>
<parameter>
<descriptor>pairgap_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Gap Penalty (Pairwise Alignment Param)</description>
<user_defined>true</user_defined>
<use_equals>true</use_equals>
</parameter>
<parameter>
<descriptor>fixedgap_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Fixed length Gap Penalty (Multiple Alignment Param)</description>
<user_defined>true</user_defined>
<use_equals>true</use_equals>
</parameter>
<parameter>
<descriptor>floatgap_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Variable length Gap Penalty (Multiple Alignment Param)</description>
<user_defined>true</user_defined>
<use_equals>true</use_equals>
</parameter>
<parameter>
<descriptor>type_STRING</descriptor>
<regex_format>([pd]+)</regex_format>
<description>Protein or DNA</description>
<user_defined>false</user_defined>
<default_value>d</default_value>
<use_equals>true</use_equals>
</parameter>
<parameter>
<descriptor>align_BOOLEAN</descriptor>
<description>Output in multifasta format</description>
<user_defined>false</user_defined>
<on>true</on>
</parameter>
<parameter>
<descriptor>transit_BOOLEAN</descriptor>
<description>Transitions not weighted (Multiple Alignment Param)</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>output_STRING</descriptor>
<regex_format>([pir]+)</regex_format>
<description>The output type (pir. gcg, clustalw)</description>
<user_defined>false</user_defined>
<default_value>gcg</default_value>
<use_equals>true</use_equals>
</parameter>
</application>
<!-- ******************** EPONINE APPLICATION BLOCK ********************* -->
<application>
<name>EPONINE</name>
<type>TRANSCRIPTION START SITE PREDICTION</type>
<path></path>
<executable>java -jar /opt/eponine/eponine-scan.jar</executable>
<format>executable -seq 1SEQUENCE(1)(1) parameter</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>true</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Thomas A. Down and Tim J. P. Hubbard. 2002</description>
<version>1</version>
<parameter>
<descriptor>threshold_STRING</descriptor>
<regex_format></regex_format>
<description>Threshold</description>
<user_defined>true</user_defined>
<default_value>0.90</default_value>
<use_equals>false</use_equals>
<dash_count>1</dash_count>
</parameter>
</application>
<!-- ******************** THERESIAS APPLICATION BLOCK ********************* -->
<application>
<name>Teiresias</name>
<type>PATTERN DISCOVERY</type>
<path>/opt/teiresias/bin</path>
<executable>teiresias_char</executable>
<format>exe_path/executable parameter -idna_sequence -ooutputfile1</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>false</results_written_to_stdout>
<output_file>
<match_name>outputfile1</match_name>
<description>Results</description>
</output_file>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Teiresias is a combinatorial pattern discovery tool developed at IBM (I.Rigoutsos and A. Floratos)</description>
<creator>http://www.research.ibm.com/bioinformatics/</creator>
<version>1</version>
<data_entry_set>
<name>dna_sequence</name>
<minimum_count>1</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.FastaToMultiFastaOutputter</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>l_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Pattern length (Number of non dot characters in a pattern)</description>
<user_defined>true</user_defined>
<default_value>3</default_value>
<parameter_value_spacing>0</parameter_value_spacing>
</parameter>
<parameter>
<descriptor>w_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Template Length</description>
<user_defined>true</user_defined>
<default_value>5</default_value>
<parameter_value_spacing>0</parameter_value_spacing>
</parameter>
<parameter>
<descriptor>c_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Convolution Length</description>
<user_defined>true</user_defined>
<default_value>2</default_value>
<parameter_value_spacing>0</parameter_value_spacing>
</parameter>
<parameter>
<descriptor>k_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Min support</description>
<user_defined>true</user_defined>
<default_value>10</default_value>
<parameter_value_spacing>0</parameter_value_spacing>
</parameter>
<parameter>
<descriptor>q_STRING</descriptor>
<regex_format>([0-9]+)</regex_format>
<description>Max Support</description>
<user_defined>true</user_defined>
<default_value>2147483647</default_value>
<parameter_value_spacing>0</parameter_value_spacing>
</parameter>
<parameter>
<descriptor>r_BOOLEAN</descriptor>
<description>Remove overlapping</description>
<user_defined>true</user_defined>
<default_value>false</default_value>
</parameter>
<parameter>
<descriptor>v_BOOLEAN</descriptor>
<description>Support metric number of occurences</description>
<user_defined>true</user_defined>
<default_value>false</default_value>
</parameter>
</application>
<!-- ******************** GIBBS SAMPLER APPLICATION BLOCK ********************* -->
<application>
<name>Lawrence Gibbs Sampler</name>
<type>MOTIF DISCOVERY</type>
<path>/opt/gibbs</path>
<executable>Gibbs.linux</executable>
<format>exe_path/executable dna_sequence parameter -o outputfile1 -n -F -y -Z</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>false</results_written_to_stdout>
<output_file>
<match_name>outputfile1</match_name>
<description>Results</description>
</output_file>
<parsing_class>ca.bcgsc.chinook.server.runner.discovery.GibbsLawrenceParser</parsing_class>
<output_path>/tmp</output_path>
<description>Lawrence Gibbs Sampler</description>
<version>1</version>
<data_entry_set>
<name>dna_sequence</name>
<minimum_count>1</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.FastaToMultiFastaOutputter</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>_STRING</descriptor>
<regex_format>\d{1,2}</regex_format>
<description>Motif length</description>
<user_defined>true</user_defined>
<default_value>10</default_value>
<use_equals>false</use_equals>
<dash_count>0</dash_count>
</parameter>
</application>
<!-- ******************** MAUVE APPLICATION BLOCK ********************* -->
<application>
<name>Mauve</name>
<type>ALIGNMENT</type>
<path>/opt/mauve</path>
<executable>Mauve_wrapper.sh</executable>
<format>exe_path/executable -out outputfile1 parameter SEQUENCE(2)(*)</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>false</results_written_to_stdout>
<output_file>
<match_name>outputfile1</match_name>
<description>Results</description>
</output_file>
<parsing_class>ca.bcgsc.chinook.server.runner.alignment.Mauve</parsing_class>
<output_path>/tmp</output_path>
<description>Mauve is developed by Aaron C. E. Darling, Bob Mau, Frederick R. Blattner, and Nicole T.Perna of the University of Wisconsin-Madison</description>
<creator>http://smweb.bcgsc.bc.ca</creator>
<version>02-19-2004</version>
<parameter>
<descriptor>-no-recursion_BOOLEAN</descriptor>
<description>Don't perform a recursive alignment</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-mums_BOOLEAN</descriptor>
<description>Find MUMs only, do not attempt to determine locally collinear blocks (LCBs)</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-no-lcb-extension_BOOLEAN</descriptor>
<description>If determining LCBs, don't attempt to extend the LCBs</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-seed-size_STRING</descriptor>
<description>Initial seed match size, default is log_2( average seq. length )</description>
<regex_format>([0-9]+)</regex_format>
<use_equals>true</use_equals>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-eliminate-inclusions_BOOLEAN</descriptor>
<description>Eliminate linked inclusions in subset matches.</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-weight_STRING</descriptor>
<description>Minimum LCB weight in base pairs per sequence.</description>
<regex_format>([0-9]+)</regex_format>
<use_equals>true</use_equals>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-max-backbone-gap_STRING</descriptor>
<description>Allow backbone to be interrupted by gaps up to this length in b.p.</description>
<regex_format>([0-9]+)</regex_format>
<use_equals>true</use_equals>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>-min-recursive-gap-length_STRING</descriptor>
<description>Minimum size of gaps that Mauve will perform recursive MUM anchoring on (Default is 200)</description>
<regex_format>([0-9]+)</regex_format>
<use_equals>true</use_equals>
<user_defined>true</user_defined>
</parameter>
</application>
<!-- ******************** PROMOTERWISE APPLICATION BLOCK ********************* -->
<!--
<application>
<name>Promoterwise</name>
<type>ALIGNMENT</type>
<path>/opt/wise2/wise2.2.3-rc7/src/bin</path>
<executable>promoterwise</executable>
<format>exe_path/executable parameter</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>WISE2 package E. Birney</description>
<version>2.2.3-rc7</version>
<parameter>
<descriptor>_FILE</descriptor>
<description>Query sequence</description>
<user_defined>true</user_defined>
<default_value></default_value>
<use_equals>false</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>_FILE</descriptor>
<description>Target sequence</description>
<user_defined>true</user_defined>
<default_value></default_value>
<use_equals>false</use_equals>
<dash_count>0</dash_count>
</parameter>
</application>
-->
<!-- ******************** SNPSEQUENCE APPLICATION BLOCK ********************* -->
<!--
<application>
<name>SNPSequence</name>
<type>VARIATION</type>
<path>/home/smontgom/bomge_perl/variation_analysis</path>
<executable>fetchSNPSequence.pl</executable>
<format>exe_path/executable parameter</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Written by Stephen Montgomery</description>
<version>1</version>
<parameter>
<descriptor>chromosome_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the chromosome</description>
<user_defined>true</user_defined>
<default_value>1</default_value>
<use_equals>false</use_equals>
<dash_count>1</dash_count>
</parameter>
<parameter>
<descriptor>start_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the start</description>
<user_defined>true</user_defined>
<default_value>1</default_value>
<use_equals>false</use_equals>
<dash_count>1</dash_count>
</parameter>
<parameter>
<descriptor>end_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the end</description>
<user_defined>true</user_defined>
<default_value>1</default_value>
<use_equals>false</use_equals>
<dash_count>1</dash_count>
</parameter>
<parameter>
<descriptor>strand_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the strand</description>
<user_defined>true</user_defined>
<default_value>1</default_value>
<use_equals>false</use_equals>
<dash_count>1</dash_count>
</parameter>
</application>
-->
<!-- ******************** SIM4 APPLICATION BLOCK ********************* -->
<application>
<name>Sim4</name>
<type>ALIGNMENT</type>
<path>/opt/sim4/sim4.2003-09-21</path>
<executable>sim4</executable>
<format>exe_path/executable dna_sequence parameter</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Sim4 Copyright Liliana Florea</description>
<version>2003-09-21</version>
<data_entry_set>
<name>dna_sequence</name>
<maximum_count>2</maximum_count>
<minimum_count>2</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>W_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the word size for blast hits (def. 12)</description>
<user_defined>true</user_defined>
<default_value>12</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>X_STRING</descriptor>
<regex_format></regex_format>
<description>Controls the limits for terminating word extensions (def. 12)</description>
<user_defined>true</user_defined>
<default_value>12</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>K_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the threshold for the MSP scores when determining basic exon cores</description>
<user_defined>true</user_defined>
<default_value>16</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>C_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the threshold for MSP scores when aligning as-yet-unmatched fragments</description>
<user_defined>true</user_defined>
<default_value>12</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>D_STRING</descriptor>
<regex_format></regex_format>
<description>Sets the bound for the diagonal distance within consecutive MSPs in an exon (def 10)</description>
<user_defined>true</user_defined>
<default_value>10</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>R_STRING</descriptor>
<regex_format></regex_format>
<description>Specified the direction of the search</description>
<user_defined>false</user_defined>
<default_value>2</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>A_STRING</descriptor>
<regex_format></regex_format>
<description>Specifies output format</description>
<user_defined>false</user_defined>
<default_value>3</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>P_STRING</descriptor>
<regex_format></regex_format>
<description>Specifies whether or not program should report fragment of alignment containing Poly-A</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>H_STRING</descriptor>
<regex_format></regex_format>
<description>Resets the MSPs weight to compensate for large introns</description>
<user_defined>true</user_defined>
<default_value>500</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
<parameter>
<descriptor>N_STRING</descriptor>
<regex_format></regex_format>
<description>Requests an additional search for small marginal exons</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
<use_equals>true</use_equals>
<dash_count>0</dash_count>
</parameter>
</application>
<!-- ******************** ORCA APPLICATION BLOCK ********************* -->
<application>
<name>Orca</name>
<type>ALIGNMENT</type>
<path>/opt/orca/ORCA</path>
<executable>orca.pl</executable>
<format>exe_path/executable -in1 dna_sequence1 -in2 dna_sequence2 parameter</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>false</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Sim4 Copyright Liliana Florea</description>
<version>2003-09-21</version>
<data_entry_set>
<name>dna_sequence1</name>
<maximum_count>1</maximum_count>
<minimum_count>1</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<data_entry_set>
<name>dna_sequence2</name>
<maximum_count>1</maximum_count>
<minimum_count>1</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>maxlen_STRING</descriptor>
<regex_format></regex_format>
<description>Maximum length of a sequence to pass to global (N-W) alignment</description>
<user_defined>true</user_defined>
<default_value>10000</default_value>
</parameter>
<parameter>
<descriptor>gms_STRING</descriptor>
<regex_format></regex_format>
<description>N-W Nucleotide match score</description>
<user_defined>true</user_defined>
<default_value>3</default_value>
</parameter>
<parameter>
<descriptor>gmms_STRING</descriptor>
<regex_format></regex_format>
<description>N-W Nucleotide mismatch score</description>
<user_defined>true</user_defined>
<default_value>-1</default_value>
</parameter>
<parameter>
<descriptor>ggop_STRING</descriptor>
<regex_format></regex_format>
<description>N-W Penalty for opening a gap</description>
<user_defined>true</user_defined>
<default_value>20</default_value>
</parameter>
<parameter>
<descriptor>ggxp_STRING</descriptor>
<regex_format></regex_format>
<description>N-W Penalty for extending a gap</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
</parameter>
<parameter>
<descriptor>gapped_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Use gapped alignment</description>
<user_defined>true</user_defined>
<default_value>1</default_value>
</parameter>
<parameter>
<descriptor>lms_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Nucleotide match score</description>
<user_defined>true</user_defined>
<default_value>1</default_value>
</parameter>
<parameter>
<descriptor>lmms_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Nucleotide mismatch score</description>
<user_defined>true</user_defined>
<default_value>-7</default_value>
</parameter>
<parameter>
<descriptor>lmmi_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Nucleotide mismatch increment</description>
<user_defined>true</user_defined>
<default_value>2</default_value>
</parameter>
<parameter>
<descriptor>lgop_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Gap open penalty</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
</parameter>
<parameter>
<descriptor>lgxp_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Gap extension penalty</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
</parameter>
<parameter>
<descriptor>expect_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn expectation value</description>
<user_defined>true</user_defined>
<default_value>0.1</default_value>
</parameter>
<parameter>
<descriptor>expect_OPTION</descriptor>
<regex_format></regex_format>
<description>Blastn expectation value</description>
<user_defined>true</user_defined>
<default_value>0.1</default_value>
<option>
<item>0.01</item>
<item>0.1</item>
<item>0.2</item>
</option>
</parameter>
<parameter>
<descriptor>xdrop_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn X dropoff value in bits</description>
<user_defined>true</user_defined>
<default_value>30</default_value>
</parameter>
<!-- <parameter>
<descriptor>hxt_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Threshold for extending hits</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
</parameter> -->
<parameter>
<descriptor>wordsize_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn Word size</description>
<user_defined>true</user_defined>
<default_value>15</default_value>
</parameter>
<parameter>
<descriptor>wsd_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn word size decrement</description>
<user_defined>true</user_defined>
<default_value>4</default_value>
</parameter>
<!-- <parameter>
<descriptor>zval_STRING</descriptor>
<regex_format></regex_format>
<description>Blastn X dropoff value for final gapped alignment</description>
<user_defined>true</user_defined>
<default_value>50</default_value>
</parameter> -->
</application>
<!-- ******************** MULTIOUT TEST APPLICATION BLOCK ****************** -->
<!--
<application>
<name>MULTIOUT</name>
<type>TEST</type>
<path>/home/smontgom/temp</path>
<executable>multiout_stdout.pl</executable>
<format>exe_path/executable -out tempfile</format>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Written by Stephen Montgomery</description>
<version>1</version>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>true</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<output_file>
<match_name>tempfile</match_name>
<description>A secondary test output file</description>
</output_file>
</application>
-->
<!-- ******************** CONTIG_MERGER TEST APPLICATION BLOCK ****************** -->
<application>
<name>Contig_Merger</name>
<type>ASSEMBLY</type>
<path>/opt/contigmerger</path>
<executable>ctg_merger_singleton_bridge</executable>
<format>exe_path/executable -f fpc_file -c cor_file -p param_file parameter -A -n outputfile</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>true</allow_stdout_preview>
<results_written_to_stdout>false</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Contig_Merger (V. Astakhova)</description>
<version>2004-11-24</version>
<output_file>
<match_name>outputfile</match_name>
<description>Results</description>
</output_file>
<data_entry_set>
<name>fpc_file</name>
<maximum_count>1</maximum_count>
<minimum_count>1</minimum_count>
<data_entry_type_name>FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<data_entry_set>
<name>cor_file</name>
<maximum_count>1</maximum_count>
<minimum_count>1</minimum_count>
<data_entry_type_name>FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<data_entry_set>
<name>param_file</name>
<maximum_count>1</maximum_count>
<minimum_count>1</minimum_count>
<data_entry_type_name>FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetOutputterImpl</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>t_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Threshold</description>
<user_defined>true</user_defined>
<default_value>1e-6</default_value>
</parameter>
<parameter>
<descriptor>u_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>u parameter</description>
<user_defined>true</user_defined>
<default_value>2</default_value>
</parameter>
<parameter>
<descriptor>E_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>E parameter</description>
<user_defined>true</user_defined>
<default_value>2</default_value>
</parameter>
</application>
<!-- ******************** CLUSTERBUSTER APPLICATION BLOCK ****************** -->
<application>
<name>Cluster-buster</name>
<type>REGULATORY MODULE PREDICTION</type>
<path>/opt/clusterbuster</path>
<executable>cbust-linux</executable>
<format>exe_path/executable parameter matrix_file dna_sequence</format>
<allow_stderr_preview>true</allow_stderr_preview>
<allow_stdout_preview>true</allow_stdout_preview>
<results_written_to_stdout>true</results_written_to_stdout>
<parsing_class>ca.bcgsc.chinook.server.runner.impl.ExecutableImpl</parsing_class>
<output_path>/tmp</output_path>
<description>Finds regulatory modules based on clusters of detected motifs (Frith et al.)</description>
<creator>http://zlab.bu.edu/cluster-buster/</creator>
<version>2003-11-18</version>
<data_entry_set>
<name>matrix_file</name>
<maximum_count>10000</maximum_count>
<minimum_count>1</minimum_count>
<data_entry_type_name>TFBS_MATRIX</data_entry_type_name>
<data_entry_type_name>FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.DataEntrySetAppendToSingleFileOutputter</set_output_class_name>
</data_entry_set>
<data_entry_set>
<name>dna_sequence</name>
<minimum_count>1</minimum_count>
<data_entry_type_name>DNA_LOCATION</data_entry_type_name>
<data_entry_type_name>DNA_FILE</data_entry_type_name>
<set_output_class_name>ca.bcgsc.chinook.parsing.setoutput.impl.FastaToMultiFastaOutputter</set_output_class_name>
</data_entry_set>
<parameter>
<descriptor>c_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Cluster Score Threshold</description>
<user_defined>true</user_defined>
<default_value>5</default_value>
</parameter>
<parameter>
<descriptor>m_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Motif Score Threshold</description>
<user_defined>true</user_defined>
<default_value>6</default_value>
</parameter>
<parameter>
<descriptor>g_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Expected gap between neigbouring motifs in a cluster</description>
<user_defined>true</user_defined>
<default_value>35</default_value>
</parameter>
<parameter>
<descriptor>r_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Range in bp for counting local nucleotide abundances</description>
<user_defined>true</user_defined>
<default_value>2</default_value>
</parameter>
<parameter>
<descriptor>l_BOOLEAN</descriptor>
<description>mask lowercase letters</description>
<user_defined>true</user_defined>
</parameter>
<parameter>
<descriptor>p_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Pseudocount</description>
<user_defined>true</user_defined>
<default_value>0.375</default_value>
</parameter>
<parameter>
<descriptor>f_STRING</descriptor>
<regex_format>[\S]+</regex_format>
<description>Output format (O: per sequence, 1: per sequence, concise, 2: sorted by cluster score, 3: sort concise)</description>
<user_defined>true</user_defined>
<default_value>0</default_value>
</parameter>
</application>
</chinook>
------------------------------------------------------------------------
#THIS FILE MUST BE IN THE CHINOOK CLASSPATH, I USUALLY COPY IT TO classes/ AFTER
#I MAKE CHANGES TO IT.
#Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=WARN, A1
#A1 is set to be a ConsoleAppender.
#log4j.appender.A1=org.apache.log4j.ConsoleAppender
log4j.appender.A2=org.apache.log4j.RollingFileAppender
log4j.appender.A2.File=chinook.log
log4j.appender.A2.MaxFileSize=1000KB
#A1, A2 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%d [%t] %-5p %c - %m%n
#log4j.appender.A2.layout=org.apache.log4j.PatternLayout
#log4j.appender.A2.layout.ConversionPattern=%d [%t] %-5p %c - %m%n
#CLASS SPECIFIC LOGGING
#Client
log4j.logger.ca.bcgsc.chinook.client=INFO
log4j.logger.ca.bcgsc.chinook.client.newgui.parameterentry=DEBUG
#P2P
log4j.logger.net.jxta=INFO
log4j.logger.ca.bcgsc.chinook.p2p=INFO
#Server
log4j.logger.ca.bcgsc.chinook.server=INFO
##Common
log4j.logger.ca.bcgsc.chinook.common=INFO
##Batching
log4j.logger.ca.bcgsc.chinook.batching=DEBUG
##Exec
log4j.logger.ca.bcgsc.chinook.exec=INFO
##Parsing
log4j.logger.ca.bcgsc.chinook.parsing=INFO
##JUnit
log4j.logger.ca.bcgsc.chinook.junit=INFO
##Ensembl
log4j.logger.org.ensembl=ERROR
##Filewire
log4j.logger.ca.bcgsc.filewire=INFO
------------------------------------------------------------------------
#THIS FILE MUST BE IN THE CHINOOK CLASSPATH, I USUALLY COPY IT TO classes/ AFTER
#I MAKE CHANGES TO IT.
#Set root logger level to DEBUG and its only appender to A1.
log4j.rootLogger=WARN, A1
#A1 is set to be a ConsoleAppender.
log4j.appender.A1=org.apache.log4j.ConsoleAppender
#A1 uses PatternLayout.
log4j.appender.A1.layout=org.apache.log4j.PatternLayout
log4j.appender.A1.layout.ConversionPattern=%d [%t] %-5p %c - %m%n
#CLASS SPECIFIC LOGGING
#Server
log4j.logger.ca.bcgsc.filewire=INFO
> (Continue).
> This is what I have.
>
> ant p2p-now
> start RMIregistry
> start Server
>
> 2004-12-14 16:03:42,984 [main] INFO
> ca.bcgsc.chinook.server.manager.ServerManager - SERVER MANAGER STARTED
> 2004-12-14 16:03:42,984 [main] INFO
> ca.bcgsc.chinook.exec.configuration.ProcessConfiguration - Reading
> process configuration file
> Chinook Server can be shutdown on port: 7337
> 2004-12-14 16:03:43,046 [main] INFO
> ca.bcgsc.chinook.server.exec.ChinookServer - Chinook Server can be
> shutdown on port: 7337
> 2004-12-14 16:03:43,062 [main] INFO
> ca.bcgsc.chinook.server.configuration.Configuration - Reading
> configuration file
> 2004-12-14 16:03:43,078 [Thread-2] INFO
> ca.bcgsc.chinook.server.manager.ServerManager - Notify that
> advertisement thread started
> 2004-12-14 16:03:43,078 [Thread-2] INFO
> ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: attempting
> connection to server
> 2004-12-14 16:03:43,125 [main] INFO
> ca.bcgsc.chinook.server.configuration.Configuration - Reading
> configuration file
> 2004-12-14 16:03:43,250 [Thread-2] INFO
> ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: Received welcome -
> WELCHIN
> 2004-12-14 16:03:43,265 [Thread-2] INFO
> ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: Sent ACK
> 2004-12-14 16:03:44,109 [main] INFO
> ca.bcgsc.chinook.server.exec.ChinookServer - Start-up as RMI -
> autostart rmiregistry
> 2004-12-14 16:03:44,156 [main] WARN
> ca.bcgsc.chinook.server.exec.ChinookServer - Registry likely already
> started, cancel autostart
> 2004-12-14 16:03:44,156 [main] INFO
> ca.bcgsc.chinook.server.exec.ChinookServer - Starting RMI service -
> ApplicationServerImpl
> 2004-12-14 16:03:44,156 [main] INFO
> ca.bcgsc.chinook.server.remote.impl.ApplicationServerImpl - Starting
> RMI service
> 2004-12-14 16:03:44,171 [main] INFO
> ca.bcgsc.chinook.server.remote.impl.ApplicationServerImpl - Obtaining
> new RMISecurityManager()
> 2004-12-14 16:03:44,328 [main] INFO
> ca.bcgsc.chinook.server.remote.impl.ApplicationServerRealImpl -
> ApplicationServerRealImpl: Instantiated
> 2004-12-14 16:03:44,328 [main] INFO
> ca.bcgsc.chinook.server.remote.impl.ApplicationServerImpl - Attempting
> to bind to rmiregistry at: //localhost:1099/ApplicationServerImpl
> 2004-12-14 16:03:44,609 [main] INFO
> ca.bcgsc.chinook.server.remote.impl.ApplicationServerImpl -
> AlignmentServerImpl bound
> 2004-12-14 16:03:44,609 [main] INFO
> ca.bcgsc.chinook.server.exec.ChinookServer - Starting RMI service -
> FireWireImpl
> 2004-12-14 16:03:44,609 [main] INFO
> ca.bcgsc.filewire.server.remote.impl.FileWireImpl - FileWireImpl:
> Instantiated for listen port: 1098
> 2004-12-14 16:03:44,609 [main] INFO
> ca.bcgsc.filewire.server.remote.impl.FileWireImpl - Starting RMI service
> 2004-12-14 16:03:44,656 [main] INFO
> ca.bcgsc.filewire.server.remote.impl.FileWireRealImpl -
> FileWireRealImpl instantiated
> 2004-12-14 16:03:44,656 [main] WARN
> ca.bcgsc.filewire.server.remote.impl.FileWireImpl -
> java.rmi.server.ServerNotActiveException: not in a remote call
> 2004-12-14 16:03:44,656 [main] INFO
> ca.bcgsc.filewire.server.configuration.Configuration - Reading
> filewire configuration file
> 2004-12-14 16:03:44,671 [main] INFO
> ca.bcgsc.filewire.server.remote.impl.FileWireImpl - Attempting to bind
> to rmiregistry at: //localhost:1099/FileWireImpl
> 2004-12-14 16:03:44,718 [main] INFO
> ca.bcgsc.filewire.server.remote.impl.FileWireImpl - FileWireImpl bound
> 2004-12-14 16:03:44,734 [main] INFO
> ca.bcgsc.chinook.server.manager.ServerManager - Notify that server started
> 2004-12-14 16:04:54,171 [RMI TCP Connection(2)-132.239.132.190] INFO
> ca.bcgsc.chinook.server.remote.impl.ApplicationServerRealImpl -
> ApplicationServerRealImpl: getApplicationTypes()
>
>
> Then
>
> ant client > Out2
>
> Client log in Out2.
>
> Vadim.
>
>------------------------------------------------------------------------
>
>Buildfile: build.xml
>
>init:
> [echo] All logging written to chinook.log
>
>compile:
> [javac] Compiling 4 source files to C:\Peer2Peer\chinook\classes
>
>jar:
> [tar] Nothing to do: C:\Peer2Peer\chinook\filesToDeploy\chinook.tar is up to date.
> [gzip] Nothing to do: C:\Peer2Peer\chinook\filesToDeploy\chinook.tar.gz is up to date.
>
>build:
>
>client:
> [echo] Starting Chinook Client
> [echo] NOTE: If you want to run in P2P mode, you will have to start the
> [echo] P2P Node before running the client.
> [java] 2004-12-14 16:08:51,109 [main] INFO ca.bcgsc.chinook.client.manager.ClientManager - CLIENT MANAGER STARTED
> [java] 2004-12-14 16:08:51,343 [main] INFO ca.bcgsc.chinook.client.manager.ServiceManager - SERVICE MANAGER STARTED
> [java] 2004-12-14 16:08:51,359 [main] INFO ca.bcgsc.chinook.batching.manager.BatchManager - BATCH MANAGER STARTED
> [java] 2004-12-14 16:08:51,359 [main] INFO ca.bcgsc.chinook.client.manager.JobManager - JOB MANAGER STARTED
> [java] 2004-12-14 16:08:51,359 [main] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - DISCOVERY MANAGER STARTED
> [java] 2004-12-14 16:08:51,921 [main] INFO ca.bcgsc.chinook.client.newgui.servicetype.DiscoveryConditionSetManager - DISCOVERY CONDITION SET MANAGER
> [java] 2004-12-14 16:08:52,984 [Thread-1] INFO ca.bcgsc.chinook.client.newgui.ChinookSplashScreen - Dispose Splash screen
> [java] 2004-12-14 16:08:53,000 [Thread-8] INFO ca.bcgsc.chinook.client.configuration.StaticServiceThread - StaticServiceThread running...
> [java] 2004-12-14 16:08:53,015 [Thread-8] INFO ca.bcgsc.chinook.client.configuration.StaticServiceConfigurationImpl - Reading static service configuration file
> [java] 2004-12-14 16:08:53,062 [Thread-9] INFO ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: attempting connection to server
> [java] 2004-12-14 16:08:53,250 [Thread-9] INFO ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: Received welcome - WELCHIN
> [java] 2004-12-14 16:08:53,281 [Thread-9] INFO ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: Sent ACK
> [java] 2004-12-14 16:08:53,390 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at f19d6e
> [java] 2004-12-14 16:08:53,437 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at 1ab600f
> [java] 2004-12-14 16:08:53,468 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at b914b3
> [java] 2004-12-14 16:08:53,468 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at fdfc58
> [java] 2004-12-14 16:08:53,484 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at c22a3b
> [java] 2004-12-14 16:08:53,484 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at f449b8
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at 178920a
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at bbfa5c
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at 131de9b
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at 10d95cd
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at e5f46e
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at 1128f5a
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at 1818f80
> [java] 2004-12-14 16:08:53,515 [Thread-11] INFO ca.bcgsc.chinook.p2p.net.discovery.DiscoveryReceiverSocketThread - Service received: ca.bcgsc.chinook.p2p.data.Service at f42160
> [java] 2004-12-14 16:08:53,937 [Thread-8] INFO ca.bcgsc.chinook.server.configuration.Configuration - Reading configuration file
> [java] 2004-12-14 16:09:18,265 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.client.newgui.servicetype.DiscoveryConditionSetManager - update the condition set and notify the DiscoveryManager
> [java] 2004-12-14 16:09:18,265 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - Discovering services by discovery condition set
> [java] 2004-12-14 16:09:18,281 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Discovery event received: 0
> [java] 2004-12-14 16:09:18,281 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Refreshing services with discovery conditions
> [java] 2004-12-14 16:09:19,437 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.client.newgui.servicetype.DiscoveryConditionSetManager - update the condition set and notify the DiscoveryManager
> [java] 2004-12-14 16:09:19,437 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - Discovering services by discovery condition set
> [java] 2004-12-14 16:09:19,437 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Discovery event received: 0
> [java] 2004-12-14 16:09:19,437 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Refreshing services with discovery conditions
> [java] 2004-12-14 16:09:20,031 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.client.newgui.servicetype.DiscoveryConditionSetManager - update the condition set and notify the DiscoveryManager
> [java] 2004-12-14 16:09:20,031 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - Discovering services by discovery condition set
> [java] 2004-12-14 16:09:20,031 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Discovery event received: 0
> [java] 2004-12-14 16:09:20,031 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Refreshing services with discovery conditions
> [java] 2004-12-14 16:09:20,828 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.client.newgui.servicetype.DiscoveryConditionSetManager - update the condition set and notify the DiscoveryManager
> [java] 2004-12-14 16:09:20,828 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - Discovering services by discovery condition set
> [java] 2004-12-14 16:09:20,828 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Discovery event received: 0
> [java] 2004-12-14 16:09:20,828 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Refreshing services with discovery conditions
> [java] 2004-12-14 16:09:21,531 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.client.newgui.servicetype.DiscoveryConditionSetManager - update the condition set and notify the DiscoveryManager
> [java] 2004-12-14 16:09:21,531 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - Discovering services by discovery condition set
> [java] 2004-12-14 16:09:21,531 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Discovery event received: 0
> [java] 2004-12-14 16:09:21,531 [Thread-6] INFO ca.bcgsc.chinook.client.newgui.services.ServicesTableModel - Refreshing services with discovery conditions
> [java] 2004-12-14 16:09:59,609 [AWT-EventQueue-0] INFO ca.bcgsc.chinook.client.manager.ClientManager - Client Stop Requested
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.p2p.net.ClientSocketThread - CST: Stopping thread
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.client.exec.ChinookClient - Controlled shutdown LEVEL 1 for client
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.client.manager.ServiceManager - SERVICE MANAGER STOPPED
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.batching.manager.BatchManager - BATCH MANAGER STOPPED
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.p2p.client.DiscoveryManager - DISCOVERY MANAGER STOPPED
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.client.manager.JobManager - JOB MANAGER STOPPED
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.client.exec.ChinookClient - Client stopped
> [java] 2004-12-14 16:09:59,640 [Thread-1] INFO ca.bcgsc.chinook.client.manager.ClientManager - CLIENT MANAGER STOPPED
>
>BUILD SUCCESSFUL
>Total time: 1 minute 45 seconds
>
>
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