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?)
Which distribution is biomart developed for?
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/registryURLPointer.xml
Or did you want me to run something else?
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
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:
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)
