Installing Newbler 2.7 on Ubuntu 12.04, java problem

[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

[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

[JackieBadger]

Thanks a lot.

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 for the input guys, appreciated.

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

Cheers

J

[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.

[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

[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.