Installing Newbler 2.7 on Ubuntu 12.04, java problem

[JackieBadger]

Hi,

I realise this question has been addressed previously but the resolutions given have not solved the issue in the versions of Newbler/Ubuntu I am using.

I am trying to install Newbler 2.7 in Ubuntu 12.04

I resolved the "rocks" error by creating a ~/bin and adding to PATH
then

ln -s /bin/true ~/bin/rocks

This launches the Nixstaller, however the following error occurs:


"Verifying checksums...

Installing jre... Failed

A complete log of this installation can be found in:
/tmp/Install_DataAnalysis_2.7_08_May_2013_1306.log

Installation failed.

See log file for details.
=========================

Click "Finish" to exit this installer. "


Detailed from error log:
"Hostname: ubuntu

=============================
[01:06:36 PM] cd /home/mgpl/programs/DataAnalysis_2.7_All; md5sum -c checksum_inst

./setup.sh: OK
./README: OK
./packages/jre-linux-i586-oracle-2.7-1.noarch.rpm: OK
./packages/gsMapper-2.7-1.noarch.rpm: OK
./packages/gsNewbler-2.7-1.i686.rpm: OK
./packages/gsSeqTools-2.7-1.x86_64.rpm: OK
./packages/gsAmplicons-2.7-1.noarch.rpm: OK
./packages/gsNewbler-2.7-1.x86_64.rpm: OK
./packages/amplicons_CLI_2.7.i686.tgz: OK
./packages/gsAssembler-2.7-1.noarch.rpm: OK
./packages/gsSeqTools-2.7-1.i686.rpm: OK
=============================

=============================
[01:06:36 PM] installRpm.sh /home/mgpl/programs/DataAnalysis_2.7_All/packages/jre-linux-i586-oracle-2.7-1.noarch.rpm /home/mgpl/454/apps/jre /home/mgpl/454 other --force --relocate /opt/454/apps/jre/jre1.6.0_30=/

/tmp/selfgz7717/files_extra//installRpm.sh: 12: /tmp/selfgz7717/files_extra//installRpm.sh: Syntax error: "(" unexpected
============================="


I realise its a java related error, and Roche is looking for jre1.6.0_30, which is not available on ubuntu.

I am running
java version "1.7.0_09"
OpenJDK Runtime Environment (IcedTea7 2.3.3) (7u9-2.3.3-0ubuntu1~12.04.1)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

How do I fool Newber around this issue?

ANy help would be much appreciated.

[sklages]

/tmp/selfgz7717/files_extra//installRpm.sh: 12: /tmp/selfgz7717/files_extra//installRpm.sh: Syntax error: "(" unexpected
============================="

This is probably due to Ubuntu using 'dash' as system shell (invoking 'sh' from within a script invokes 'dash'). Just configure the default system shell being 'bash'. I always do this since 10.04; no performance loss, but less problems with '#!/bin/sh' stuff ;-)

I realise its a java related error, and Roche is looking for jre1.6.0_30, which is not available on ubuntu.

I am running
java version "1.7.0_09"
OpenJDK Runtime Environment (IcedTea7 2.3.3) (7u9-2.3.3-0ubuntu1~12.04.1)
OpenJDK 64-Bit Server VM (build 23.2-b09, mixed mode)

Get the java JRE/SDK directly from oracle [1] and install it somewhere in your 454 directory structure; change the scripts accordingly to use this specific version of java.

Think about subsituting your openJDK with with Oracle's java 7 systemwide; it is said that performance is better ...

EDIT: hmm, Roche brings its own (32bit) version of java 6. Seems that java 7 is not your problem. Just fix the dash/bash stuff and then see if it works.
For my Roche installations on 64bit Ubuntu I use Oracle's java .. you don't necessarily need it.

java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01, mixed mode)

hth,
Sven

[1]=http://www.oracle.com/technetwork/java/javase/downloads/index.html

[ajthomas]

You might be running into Java issues that I ran across back when I first tried to install the 454 software in Fedora. It worked fine in 32-bit Fedora, but couldn't find Java in 64-bit Fedora. After a bit of back and forth with Roche, they came up with some additional libraries that need to be installed. The installer now tells the user to install those libraries when it discovers that they're needed. I remember one is zlib.i386, but I don't remember the others off the top of my head. I know it's been posted more than once here (try the 454 subforum). You might just need those libraries to solve your problem.

[JackieBadger]

Thanks for the input guys, appreciated.

One more Q.
How do I "configure the default system shell being 'bash' " ?

Cheers

J

[GenoMax]

How do I "configure the default system shell being 'bash' " ?

Cheers

J

Procedure is described here. Replace with the path for a shell you want to use.

http://ubuntuforums.org/showthread.php?t=2050679

[JackieBadger]

Thanks a lot.

J

[sklages]

Thanks for the input guys, appreciated.

One more Q.
How do I "configure the default system shell being 'bash' " ?

Cheers

J

You don't want to change your login shell, but the system shell:

http://wiki.ubuntuusers.de/Dash

$ sudo dpkg-reconfigure dash

This is asking you if you want to use 'dash' for '/bin/sh'. Answer 'no' to use 'bash' instead.

hth,
Sven

[sklages]

You might be running into Java issues that I ran across back when I first tried to install the 454 software in Fedora. It worked fine in 32-bit Fedora, but couldn't find Java in 64-bit Fedora. After a bit of back and forth with Roche, they came up with some additional libraries that need to be installed. The installer now tells the user to install those libraries when it discovers that they're needed. I remember one is zlib.i386, but I don't remember the others off the top of my head. I know it's been posted more than once here (try the 454 subforum). You might just need those libraries to solve your problem.

If you run into problems with their 32bit java, I'd install my own 64bit oracle java somewhere in the Roche Software tree and alter the corresponding five or so scripts to use that java.

btw, I never installed libs like zlib.i386 which is Roche moaning about; installation proceeds without them.

Sven

[JackieBadger]

You don't want to change your login shell, but the system shell:

http://wiki.ubuntuusers.de/Dash

$ sudo dpkg-reconfigure dash

This is asking you if you want to use 'dash' for '/bin/sh'. Answer 'no' to use 'bash' instead.

hth,
Sven

Thanks!
This worked..and installation completed with no apparent issues.
Appreciate the help guys!

[JackieBadger]

OK...

So I managed to get the program working on my own machine, but the assembly maxed out the RAM (~29GB in a virtual machine). As such I am trying to now install on a linux dedicated machine that has 64GB.

But I am running into problems again.

The installer says I lack the libraries zlib:i386 Lib xi:i386 Lib xtst:i386 and LibXaw:i386

I can not remember how I installed these on my personal cpu a couple of years ago and am now struggling to find a source for these. It seems they are now obsolete??

If I continue with installation and ignore these, I get the following error when atempting to run gsMapper. Any solution for a non-linux boffin would be very much appreciated

"mgplab@new2012:~/454/apps/mapper/bin$ ./gsMapper
Exception in thread "main" java.lang.UnsatisfiedLinkError: /home/mgplab/454/apps/jre/jre1.6.0_30/lib/i386/xawt/libmawt.so: libXi.so.6: cannot open shared object file: No such file or directory
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.load0(Unknown Source)
at java.lang.System.load(Unknown Source)
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(Unknown Source)
at java.lang.ClassLoader.loadLibrary(Unknown Source)
at java.lang.Runtime.loadLibrary0(Unknown Source)
at java.lang.System.loadLibrary(Unknown Source)
at sun.security.action.LoadLibraryAction.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.loadLibraries(Unknown Source)
at java.awt.Toolkit.<clinit>(Unknown Source)
at java.awt.Rectangle.<clinit>(Unknown Source)
at com.fourfivefour.ui.Resources.<clinit>(Resources.java:47)
at com.fourfivefour.ui.ResourceFactory.getNewInstance(ResourceFactory.java:79)
at com.fourfivefour.ui.ResourceFactory.get(ResourceFactory.java:66)
at com.fourfivefour.assembly.MapperMain.<clinit>(MapperMain.java:30)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at com.simontuffs.onejar.Boot.run(Boot.java:340)
at com.simontuffs.onejar.Boot.main(Boot.java:166)
"

[ajthomas]

In Red Hat/Fedora, it's as simple as "yum install zlib.i386..." I don't use Ubuntu, but as i understand, the installation procedure is similar. This thread says to install ia32-libs to get them. Not having done this on Ubuntu myself, however, I can't offer any more help than that.

[JackieBadger]

I actually just tracked the memory usage during while gsMapper indexed the reference reads. The program crashes stating it is out of memory at ~50% of the total available RAM. i.e. ~14GB RAM.

I wonder why this is? Is there anyway to open gsMapper telling it to use all 29GBs?

[sklages]

What system are you using for the real 64GB machine?
Go and get Oracle's 64bit Java 6 SDK/JRE, put it somewhere under /home/mgplab/454/, make it known to the scripts and give it a try .. :-)

Roche's suite is a mixture of 32 and 64bit software, .. one step towards 64bit ;-)

[sklages]

I actually just tracked the memory usage during while gsMapper indexed the reference reads. The program crashes stating it is out of memory at ~50% of the total available RAM. i.e. ~14GB RAM.

I wonder why this is? Is there anyway to open gsMapper telling it to use all 29GBs?

No idea if there could be any issues with the VM itself. Maybe some limits:

ulimit -a

should give you a hint about that.

[JackieBadger]

What system are you using for the real 64GB machine?
Go and get Oracle's 64bit Java 6 SDK/JRE, put it somewhere under /home/mgplab/454/, make it known to the scripts and give it a try .. :-)

Roche's suite is a mixture of 32 and 64bit software, .. one step towards 64bit ;-)

Im using Ubuntu. OK..Ill but the java executables in the 454 tree and take a look at the scripts to edit.
Thanks again