Re: [base] basedb-users Digest, Vol 70, Issue 1
One source for the problem is that the underlying RMAExpressConsole program doesn't handle ST arrays, or maybe treats ST arrays differently. Have you checked with the author of RMAExpress tool? The se.lu.thep.affymetrix for BASE plug-in and expects the output file from RMAExpressConsole to be rma.txt. Either RMAExpressConsole crashes or does not create rma.txt but rather something else. I cannot test anything myself since we do not have any ST array data nor a running BASE 2 server (which is required for the affymetrix plug-in). I suggest that you try to run RMAExpressConsole manually on your server and see what the outcome is. Are ST arrays accepted by RMAExpressConsole, does RMAExpressConsole crash (this should be caught by the plug-in), is another set of output files created for ST arrays? (Another thing to check is what files and directories are created by the plug-in once it is finished but unfortunately this is harder to accomplish since the affymetrix plug-in cleans up after it finishes.) Jari On 2015-03-11 01:01, Ross Chapman wrote: Hi Jari Thank you for your comments. I am using BASE 2.17.2 which is running on a Linux/Ubuntu server. I have found that RMAExpress runs perfectly with most Affymetrix files, but I get this error when analysing data from Affymetrix GeneChip Human Gene 1.0 ST or Affymetrix GeneChip Mouse Gene 1.0 ST arrays, so I believe that the error must lie with the configuration of the ST arrays within base. I preloaded the probes as reporters into the database from a cdf file for each array, and the reporters are visible in the database. Yet somehow the RMAExpress plugin is failing with these arrays. I would appreciate any comments or suggestions. Thanks Ross On 5 March 2015 at 00:18, basedb-users-requ...@lists.sourceforge.net mailto:basedb-users-requ...@lists.sourceforge.net wrote: Send basedb-users mailing list submissions to basedb-users@lists.sourceforge.net mailto:basedb-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/basedb-users or, via email, send a message with subject or body 'help' to basedb-users-requ...@lists.sourceforge.net mailto:basedb-users-requ...@lists.sourceforge.net You can reach the person managing the list at basedb-users-ow...@lists.sourceforge.net mailto:basedb-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of basedb-users digest... Today's Topics: 1. Re: BASE reporter fields problem (Nicklas Nordborg) 2. BASE 3.4 has been released (Nicklas Nordborg) 3. RMAexpress (Ross Chapman) 4. Re: RMAexpress (Jari H?kkinen) 5. BASE 3.4.1 has been released (Nicklas Nordborg) 6. (no subject) (Ross Chapman) 7. Re: Problem with RMAexpress plugin [Was: (no subject)] (Jari H?kkinen) -- Forwarded message -- From: Nicklas Nordborg nicklas.nordb...@med.lu.se mailto:nicklas.nordb...@med.lu.se To: BASE ML basedb-users@lists.sourceforge.net mailto:basedb-users@lists.sourceforge.net Cc: Date: Mon, 12 Jan 2015 07:50:46 +0100 Subject: Re: [base] BASE reporter fields problem On 2015-01-12 07:25, Ross Chapman wrote: Hi all I recently moved a BASE2 database to a new server by copying the full database and all installation files along with plugin files. When I try to run some custom plugins on the new instance, I receive an error stating that there is an unknown reporter field being requested in the new database version. The same plugins still work fine on the original BASE2 application. Can you point me to where the reporter fields are set and how I can correct the annotations in the new instance. This should be in the extended-properties.xml file that is found in the WEB-INF/classes directory in your BASE installation. See http://base.thep.lu.se/chrome/__site/latest/html/appendix/__extendedproperties.html http://base.thep.lu.se/chrome/site/latest/html/appendix/extendedproperties.html for some more information. /Nicklas -- Forwarded message -- From: Nicklas Nordborg nicklas.nordb...@med.lu.se mailto:nicklas.nordb...@med.lu.se To: BASE ML basedb-users@lists.sourceforge.net mailto:basedb-users@lists.sourceforge.net, BASE dev basedb-de...@lists.sourceforge.net mailto:basedb-de...@lists.sourceforge.net, basedb-annou...@lists.sourceforge.net mailto:basedb-annou...@lists.sourceforge.net Cc: Date: Wed, 14 Jan 2015 14:41:58 +0100 Subject: [base] BASE 3.4 has been released Hello all, After fixing a few issues with the beta version, BASE 3.4.0 has now
Re: [base] basedb-users Digest, Vol 70, Issue 1
On 2015-03-12 09:24, Jari Häkkinen wrote: One source for the problem is that the underlying RMAExpressConsole program doesn't handle ST arrays, or maybe treats ST arrays differently. I meant to say that problem may be with RMAExpressConsole but I don't know. Jari -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject unsubscribe to basedb-users-requ...@lists.sourceforge.net
Re: [base] basedb-users Digest, Vol 70, Issue 1
Hi Jari Thank you for your comments. I am using BASE 2.17.2 which is running on a Linux/Ubuntu server. I have found that RMAExpress runs perfectly with most Affymetrix files, but I get this error when analysing data from Affymetrix GeneChip Human Gene 1.0 ST or Affymetrix GeneChip Mouse Gene 1.0 ST arrays, so I believe that the error must lie with the configuration of the ST arrays within base. I preloaded the probes as reporters into the database from a cdf file for each array, and the reporters are visible in the database. Yet somehow the RMAExpress plugin is failing with these arrays. I would appreciate any comments or suggestions. Thanks Ross On 5 March 2015 at 00:18, basedb-users-requ...@lists.sourceforge.net wrote: Send basedb-users mailing list submissions to basedb-users@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/basedb-users or, via email, send a message with subject or body 'help' to basedb-users-requ...@lists.sourceforge.net You can reach the person managing the list at basedb-users-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than Re: Contents of basedb-users digest... Today's Topics: 1. Re: BASE reporter fields problem (Nicklas Nordborg) 2. BASE 3.4 has been released (Nicklas Nordborg) 3. RMAexpress (Ross Chapman) 4. Re: RMAexpress (Jari H?kkinen) 5. BASE 3.4.1 has been released (Nicklas Nordborg) 6. (no subject) (Ross Chapman) 7. Re: Problem with RMAexpress plugin [Was: (no subject)] (Jari H?kkinen) -- Forwarded message -- From: Nicklas Nordborg nicklas.nordb...@med.lu.se To: BASE ML basedb-users@lists.sourceforge.net Cc: Date: Mon, 12 Jan 2015 07:50:46 +0100 Subject: Re: [base] BASE reporter fields problem On 2015-01-12 07:25, Ross Chapman wrote: Hi all I recently moved a BASE2 database to a new server by copying the full database and all installation files along with plugin files. When I try to run some custom plugins on the new instance, I receive an error stating that there is an unknown reporter field being requested in the new database version. The same plugins still work fine on the original BASE2 application. Can you point me to where the reporter fields are set and how I can correct the annotations in the new instance. This should be in the extended-properties.xml file that is found in the WEB-INF/classes directory in your BASE installation. See http://base.thep.lu.se/chrome/site/latest/html/appendix/ extendedproperties.html for some more information. /Nicklas -- Forwarded message -- From: Nicklas Nordborg nicklas.nordb...@med.lu.se To: BASE ML basedb-users@lists.sourceforge.net, BASE dev basedb-de...@lists.sourceforge.net, basedb-annou...@lists.sourceforge.net Cc: Date: Wed, 14 Jan 2015 14:41:58 +0100 Subject: [base] BASE 3.4 has been released Hello all, After fixing a few issues with the beta version, BASE 3.4.0 has now been released. One new feature is the possibility to install skins. Check out the example skins at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.skincollection For a complete list of changes, see: http://base.thep.lu.se/query?milestone=BASE+3.4group=type Installation/upgrade instructions: http://base.thep.lu.se/chrome/site/latest/html/admin/installation.html As usual, the program can be downloaded from: http://base.thep.lu.se/wiki/DownloadPage /Nicklas -- Forwarded message -- From: Ross Chapman ross.chap...@mimr-phi.org To: basedb-users@lists.sourceforge.net Cc: Date: Tue, 3 Feb 2015 16:55:30 +1100 Subject: [base] RMAexpress Hi all I am having problems running the RMAexpress plug in after migrating BASE2 to a new server. The plug in fails with the following error: java.io.IOException: Unexpected exit of RMAExpress sub-process. Return value: 127 at se.lu.thep.affymetrix.RMAExpress.runBinary(RMAExpress.java:156) at se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run(AbstractExternalBinaryPlugin.java:262) at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:116) at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:510) at java.lang.Thread.run(Thread.java:745) Can you suggest a possible cause and solution? Many thanks Ross -- Dr Ross Chapman Senior Bioinformatician MIMR-PHI Institute of Medical Research 27-31 Wright Street, Clayton, VIC 3168 (03) 99024766 -- Forwarded message -- From: Jari Häkkinen jari.hakki...@med.lu.se To: basedb-users@lists.sourceforge.net Cc: Date: Tue, 03 Feb 2015 14:20:45 +0100 Subject: Re: [base] RMAexpress Hi, Did you also move the underlying RMAexpress binary to the new server? You probably need to recompile RMAExpress (http://rmaexpress.bmbolstad.com/) for your new server. Jari On
