> After installing the apt-probeset-summarize plugin and the > affymetrix.jar I tried to create a new root bioassay set using the > Plier > plugin. It failed and threw the error shown below. I noted the "PLIER > plug-in" directory that was created in the tomcat temp directory does > not conform the usual Unix convention of having no spaces in the file > name. Is this normal?
It may be a little unorthodox, but the "RMAExpress plugin" does the same thing and that works, so this behaviour is not the root of problem. Note that the path is quoted, so it is safe to use. My guess is either the entire directory tree is not executable (listable) by the user BASE2/tomcat runs as, and/or the apt-probeset- summarize binary does not have read/execute permissions for that user. Or it's not in the directory at all... On a side note, the APT 1.8/1.6 _Solaris_ binaries (1.8 temporarily pulled because of a bug hopefully irrelevant to BASE) are linked to an older version of the stdc++ library (libstdc++.so.5), which is not present on Solaris 10. Moreover, the 1.8 make procedure seems broken (complains about missing endif in Makefile.deps). APT 1.6, however, compiles nicely on Solaris 10 using: $ cd <apt-source-dir>/sdk $ configure --without-cppunit $ gmake apt-probeset-summarize can then be copied from <apt-source>/sdk/ output/<arch>/bin/. This executes successfully through the PLIER plugin (yay!). /Emil > > Thanks, > > Jim Collett > Pacific Northwest National Laboratory > > > > > java.io.IOException: Cannot run program > "/usr/local/base2/base-2.2.2/www/plugins/se/lu/thep/affymetrix/apt- > probe > set-summarize" (in directory > "/usr/tomcat/apache-tomcat-5.5.20/temp/PLIER plug-in/159"): > java.io.IOException: error=13, Permission denied > at java.lang.ProcessBuilder.start(ProcessBuilder.java:459) > at java.lang.Runtime.exec(Runtime.java:593) > at se.lu.thep.affymetrix.Plier.runPlier(Plier.java:357) > at se.lu.thep.affymetrix.Plier.run(Plier.java:310) > at > net.sf.basedb.core.PluginExecutionRequest.invoke > (PluginExecutionRequest. > java:88) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run > (InternalJobQueue.java: > 420) > at java.lang.Thread.run(Thread.java:619) > Caused by: java.io.IOException: java.io.IOException: error=13, > Permission denied > at java.lang.UNIXProcess.<init>(UNIXProcess.java:148) > at java.lang.ProcessImpl.start(ProcessImpl.java:65) > at java.lang.ProcessBuilder.start(ProcessBuilder.java:452) > ... 6 more > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > [EMAIL PROTECTED] ________________________________ Emil Lundberg / Sysadm Linnaeus Centre for Bioinformatics Uppsala University [EMAIL PROTECTED] ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
