arb installation
download arb software from the following link.
swarm probs
[INFO] [jar:jar {execution: default-jar}] [INFO] Preparing exec:java [WARNING] Removing: java from forked lifecycle, to prevent recursive invocation. [INFO] No goals needed for project - skipping [INFO] [exec:java {execution: default}] 11:05:36,441 DEBUG JobClient2:134 - 2011-01-26 11:05:36 JavaDaemonTest started 11:05:36,443 DEBUG JobClient2:134 - 2011-01-26 11:05:36 2011-01-26 11:05:36 This is output to StdErr… 11:05:36,906 DEBUG PropertyUtil:33 - L1 11:05:36,914 DEBUG PropertyUtil:35 - L2 11:05:36,914 DEBUG PropertyUtil:39 - L3 11:05:45,709 DEBUG JobManager:742 - Job Submission Thread is running… 11:05:45,807 DEBUG Programs:32 - Getting the list of jobs waiting to be submitted 11:06:21,839 DEBUG JobManager:289 - Submitting 8 jobs 11:06:21,843 DEBUG SwarmUtil:156 - Requesting ticket now 11:06:21,870 DEBUG SwarmUtil:162 - org.apache.axis2.rpc.client.RPCServiceClient@1 11:06:28,330 DEBUG SwarmUtil:166 - Ticket request result: Username: qdong Email: Default email address Project: GSA Project Organization: default organization Group Job Title: default job title Group Job Descriptiondefault job description Expected Number of Jobs130000 Timestamp: Wed Jan 26 11:06:27 CST 2011 TicketID-743724069 Current number of jobs submitted0 11:06:28,357 DEBUG JobManager:258 - ticketID : -743724069 11:06:28,742 DEBUG JobManager:204 - 1017 RepeatMasker [INFO] ———————————————————————— [ERROR] BUILD ERROR [INFO] ———————————————————————— [INFO] An exception occured while executing the Java class. org/biojava/bio/BioException
useful links
http://ycombinator.com/ http://www.reddit.com/ http://www.catb.org/~esr/faqs/hacker-howto.html http://slashdot.org/ http://www.crunchgear.com/ http://www.wired.com/ http://www.engadget.com/ http://lifehacker.com/ http://techcrunch.com/ http://download.oracle.com/javase/6/docs/api/index.html http://www.javabeginner.com/
running batch jobs on talon cluster ----> RepeatMasker
#!/bin/bash DIR=/users/prm0080/RepeatMasker/RepeatMasker/HMP_Bacteria_ContigCombine2 J=0 K=1 for i in $DIR/* do files[$J]=$i let J=$J+$K done #BSUB -J “jobArray[1-560]” #BSUB -n 1 #BSUB -M 2 #BSUB -e mothur.%J.err output error file; %J=job number
$LSB_JOBINDEX
#Run the application /users/prm0080/RepeatMasker/RepeatMasker/RepeatMasker ${files[$LSB_JOBINDEX]} -dir $DIR/suresh/
java stuff...
java blocking queue… producer and consumer..
finding for a text in files..
find . -type f -exec grep -l “cglbake” /dev/null {} +
nlp project
Polarity Detection of movie reviews Introduction :- Today, very large amounts of information are available in on-line documents. As part of the effort to better organize this information for users, researchers have been actively investigating the problem of automatic text categorization. In Polarity detection in movie reviews, The basic problem is to classify a movie review as positive or negative. Some training data set is provided and we have to develop the best technique to classify them into their respective classes. This would be very useful in knowing the defects in a product. If a customer had decided to purchase a product and is willing to know only the defects of a product rather than concentrating on parts which emphasize it. This classification process would be very helpful. Similarly we have many other scenarios like ad generation which would depend on polarity detection.
learn programming by having challenges,
ruby quiz
hadoop file system..
hadoop is platform for performing distributed computing…
error in creating session..
org.hibernate.HibernateException: Could not parse configuration: /hibernate.cfg.xml at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:1494) at org.hibernate.cfg.Configuration.configure(Configuration.java:1428) at org.hibernate.cfg.Configuration.configure(Configuration.java:1414) at com.mycompany.app.db.HibernateSessionFactory.
(HibernateSessionFactory.java:30) at com.mycompany.entity.Programs.getProgramsWaitingForSubmission2(Programs.java:33) at com.mycompany.app.job.JobManager.runJobSubmissions(JobManager.java:744) at com.mycompany.app.clients.JobClient2.runJobs(JobClient2.java:102) at com.mycompany.app.clients.JobClient2.access$000(JobClient2.java:18) at com.mycompany.app.clients.JobClient2$4.run(JobClient2.java:87) Caused by: org.dom4j.DocumentException: Error on line 2 of document : The processing instruction target matching "[xX][mM][lL]" is not allowed. Nested exception: The processing instruction target matching "[xX][mM][lL]" is not allowed. at org.dom4j.io.SAXReader.read(SAXReader.java:482) at org.hibernate.cfg.Configuration.doConfigure(Configuration.java:1484) ... 8 more %%%% Error Creating SessionFactory %%%% org.hibernate.HibernateException: /var/www/site31/swarmapp/src/main/resources/hibernate.cfg.xml not found at org.hibernate.util.ConfigHelper.getResourceAsStream(ConfigHelper.java:147) at org.hibernate.cfg.Configuration.getConfigurationInputStream(Configuration.java:1405) at org.hibernate.cfg.Configuration.configure(Configuration.java:1427) at com.mycompany.app.db.HibernateSessionFactory.rebuildSessionFactory(HibernateSessionFactory.java:94) at com.mycompany.app.db.HibernateSessionFactory.getSession(HibernateSessionFactory.java:72) at com.mycompany.entity.Programs.getProgramsWaitingForSubmission2(Programs.java:33) at com.mycompany.app.job.JobManager.runJobSubmissions(JobManager.java:744) at com.mycompany.app.clients.JobClient2.runJobs(JobClient2.java:102) at com.mycompany.app.clients.JobClient2.access$000(JobClient2.java:18) at com.mycompany.app.clients.JobClient2$4.run(JobClient2.java:87)