Hi Joel On Fri, 2007-08-24 at 14:01 +0200, Joel Hedlund wrote: > Hi! > > > You apache doesnt have apxs or apxs2 in the same directory or you dont > > have it at all. > > True. Fixed it by installing the apache2-threaded-dev package on Ubuntu > 7.04 (Feisty). > > > you need to have this under same directory as of 'httpd' or create a > > symlink if its somewhere else. > > OK. apxs2 gets installed under /usr/bin/apxs2 un Ubuntu so I symlinked > it as advised. (IHMO the location of apxs2 should be configurable so > that people won't have to meddle with dirs that that are considered > under the control of the package manager. Also, perhaps the configure > script should be adjusted to fall back to the apxs2 that is on the path > if it cannot find it in the same dir as httpd?)
Its an APACHE extension tool, so may live anywhere, however with most of the distributions, normal practise is to keep it in the same directory as httpd. > > Which distribution is biomart developed for? for all :) > > > You need apxs or apxs2 (apache extension tool) and help is > > provided in detailed documentation. > Check. It's not that easy to find though, since this prerequisite for > biomart-perl installation is only described in section 2.4.1.1 "Apache > installation for MartView", so people that already have Apache installed > will probably skip this section. IMHO this dependence should also be > mentioned under some other section, such as for example 2.4.1 > "Prerequisites". > > > for uninitialised warnings , please uncomment line 83 of > > bin/configureBioMart.pl and see what gets printed on screen. > > I did that and there was no change in the output from > > $ perl bin/configure.pl -r conf/registryURLPoi88nter.xml > > Or did you want me to run something else? thats fine, ignore it, it was for another anticipated problem. > > After installing apxs2 and symlinking I get this (looks OK?): > > > $ perl bin/configure.pl -r conf/registryURLPointer.xml > > > > Do you want to install in API only mode [y/n] [n]: > > > > Checking prerequisites ...[Looks good] > > > > APACHE: /usr/sbin/apache2 > > HOST: localhost > > PORT: 9002 > > PROXY: > > LOCATION: biomart > > > > You can change the above configuration by editing > > "biomart-perl/conf/settings.conf" > > > > > > > > Got usable Apache in /usr/sbin/apache2, probing for version & ModPerl > > configuration > > Have Apache DSO-support and ModPerl library file present, configuring > > ModPerl in httpd.conf. > > Libdir /media/sda8/yohell/download/biomart/biomart-perl/lib is not in @INC, > > adding to @INC > > > > Processing Cached Registry: > > /media/sda8/yohell/download/biomart/biomart-perl/conf/cachedRegistries/registryURLPointer.xml.cached > > But then apache won't start: > > > $ /usr/sbin/apache2 -d $PWD -f $PWD/conf/httpd.conf > > Syntax error on line 7 of > > /yolocal/download/biomart/biomart-perl/conf/httpd.conf: > > Invalid command 'MinSpareServers', perhaps misspelled or defined by a > > module not included in the server configuration StartServers MinSpareServers MaxSpareServers ServerLimit MaxClients MaxRequestsPerChild all the above directive comes from apache 'prefork.c' module which is usually included in apache default installation. > > I could not find any references to this error message in the docs. > However if I just comment out the corresponding lines in httpd.conf > (7-8) then apache seems to start just fine and I can access and use > MartView by pointing my browser at > > http://localhost:9002/biomart/martview > > but then when trying to create a new mart using MartBuilder I get a > NullPointerException once I connect to the database, and the resulting > schema view is empty. I expected to see one dummy table biomart_test > with some example data created this way: Our MartBuilder expert Richard would write to you about this problem soon. thanks for your patience and useful feedback, we will certainly look into this and do necessary amendments. syed > As root: > mysql> create database biomart_test; > Query OK, 1 row affected (0.02 sec) > > mysql> grant all on biomart_test.* to yohell; > Query OK, 0 rows affected (0.04 sec) > > As yohell: > mysql> insert into protein values ('APA_HUMAN', 'Sample protein'), > ('BEAR_HUMAN', 'Example protein'); > Query OK, 2 rows affected (0.00 sec) > Records: 2 Duplicates: 0 Warnings: 0 > > The stack trace is included below, in case it can be of interest. > > Cheers! > /Joel > > > java.lang.NullPointerException > > at > > org.biomart.builder.view.gui.diagrams.components.SchemaComponent.getName(SchemaComponent.java:228) > > at com.sun.java.swing.plaf.gtk.GTKStyle.getInsets(GTKStyle.java:263) > > at > > javax.swing.plaf.synth.SynthStyle.installDefaults(SynthStyle.java:876) > > at > > javax.swing.plaf.synth.SynthLookAndFeel.updateStyle(SynthLookAndFeel.java:252) > > at javax.swing.plaf.synth.SynthPanelUI.updateStyle(SynthPanelUI.java:70) > > at > > javax.swing.plaf.synth.SynthPanelUI.installDefaults(SynthPanelUI.java:57) > > at javax.swing.plaf.basic.BasicPanelUI.installUI(BasicPanelUI.java:39) > > at javax.swing.plaf.synth.SynthPanelUI.installUI(SynthPanelUI.java:37) > > at javax.swing.JComponent.setUI(JComponent.java:668) > > at javax.swing.JPanel.setUI(JPanel.java:136) > > at javax.swing.JPanel.updateUI(JPanel.java:109) > > at javax.swing.JPanel.<init>(JPanel.java:69) > > at javax.swing.JPanel.<init>(JPanel.java:92) > > at javax.swing.JPanel.<init>(JPanel.java:100) > > at > > org.biomart.builder.view.gui.diagrams.components.BoxShapedComponent.<init>(BoxShapedComponent.java:158) > > at > > org.biomart.builder.view.gui.diagrams.components.SchemaComponent.<init>(SchemaComponent.java:74) > > at > > org.biomart.builder.view.gui.diagrams.AllSchemasDiagram.doRecalculateDiagram(AllSchemasDiagram.java:71) > > at org.biomart.builder.view.gui.diagrams.Diagram$6.run(Diagram.java:657) > > at org.biomart.common.view.gui.LongProcess$2.run(LongProcess.java:98) > > at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199) > > at java.awt.EventQueue.dispatchEvent(EventQueue.java:597) > > at > > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273) > > at > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183) > > at > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:177) > > at java.awt.Dialog$1.run(Dialog.java:1039) > > at java.awt.Dialog$3.run(Dialog.java:1091) > > at java.security.AccessController.doPrivileged(Native Method) > > at java.awt.Dialog.show(Dialog.java:1089) > > at javax.swing.JOptionPane.showOptionDialog(JOptionPane.java:853) > > at javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:779) > > at javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:741) > > at javax.swing.JOptionPane.showConfirmDialog(JOptionPane.java:702) > > at > > org.biomart.common.view.gui.dialogs.StackTrace.showStackTrace(StackTrace.java:79) > > at org.biomart.common.view.gui.LongProcess$3.run(LongProcess.java:102) > > at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) > > at java.awt.EventQueue.dispatchEvent(EventQueue.java:597) > > at > > java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273) > > at > > java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183) > > at > > java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173) > > at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168) > > at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160) > > at java.awt.EventDispatchThread.run(EventDispatchThread.java:121) > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
