[Bio-Linux] GeneSpring version 7.3 available for Bio-Linux - not an automatic update

[Bela Tiwari]

Hello Bio-Linux System Administrators,

This message will only be pertinent to those of you running GeneSpring on your Bio-Linux machines.

Version 7.3 of GeneSpring is now available for Bio-Linux. We recommend that you upgrade as soon as possible as there are many new features in this version and users will not be able to load new data into Signet (aka GeneSpring Workgroup), the associated database, until they are running version 7.3 of GeneSpring.

The new version of GeneSpring will NOT be installed via automatic nightly update. We have done this to make sure that system administrators have the chance to back up their data before proceeding. The easiest way to proceed with the installation is to log on as manager and type:

sudo apt-get update

and then type

sudo apt-get install bio-linux-genespring

Our  web documentation for GeneSpring has been updated. Of particular importance are changes we have implemented with regards to file permissions. Please read the following information on our FAQ to make sure you understand the default setup for the new version of GeneSpring:

http://envgen.nox.ac.uk/envgen/software/archives/000366.html#permissions 


There are several issues to be aware of BEFORE proceeding with the upgrade of GeneSpring:

1) We HIGHLY recommend that you back up your GeneSpring data directory before starting the upgrade. The data directory on a default Bio-Linux machine is at /home/db/SiliconGenetics/GeneSpring/data.  The NEBC is not responsible for any of your data, so please ensure you back up.

2) Our experience has been that version 7.3 of GeneSpring works on Bio-Linux when installed on a "clean" system.  It also works when upgrading - that is, installing on a machine where GeneSpring is already in use.  However, on one of the machines I upgraded at the NEBC, I did see a conflict, where GeneSpring reported that it could not recognise the normalization scenario I was using. 
To solve this, I moved my "old" GeneSpring/data directory elsewhere and installed the new version of GeneSpring. This creates a new GeneSpring/data directory into which I then moved important files from the old version.
I cannot say what the root cause of this was, but on the basis of this, you may wish to consider "backing up" your old data directory by moving it somewhere else, installing the new bio-linux-genespring package, and then copying your user's files (and your LicenseKey.txt file) from the old GeneSpring/data folder into the new one.  I can't say whether this is really necessary or not, but I have my suspicions that things may work better this way. You'll have to decide for yourself whether to believe my hunch about this or not. Sorry I cannot provide any more concrete advice about this.

3) Agilent has not officially released GeneSpring 7.3 for Linux. As GeneSpring is a java file, it should work fine on any platform. We have endeavored to test the bio-linux-genespring package, but exhaustive testing of version 7.3 has not been done on the Linux platform by Agilent. 

If you do notice anything strange about how GeneSpring is running, please let us know. If it is problem with our package, we will fix it and alert other users right away. If it is a problem with Agilent's software, we will inform them immediately. 


Please do contact us (helpdesk at envgen.nox.ac.uk) if you experience any problems with the new version of GeneSpring.


best wishes,

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************



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