[westerman]

I've run as non-root forever. I do not recall any special problems in not being root. That being said, bioscope is hard to get set up properly. Especially with the .ini files. But none of it needs to be installed in system directories.

[mbblack]

I've run as non-root forever. I do not recall any special problems in not being root. That being said, bioscope is hard to get set up properly. Especially with the .ini files. But none of it needs to be installed in system directories.

I never said it needs to be installed as root or in any particular place. I just think that for anyone completely new to the software, having it installed as root and following ABI's suggested installation guide will make things simpler and more straightforward to get up and running with BioScope.

I have BioScope and LifeScope on our cluster installed as mentioned above, and it was relatively simple and quick to actually get working with them that way, rather than spend a lot of time editing config files and *.ini files and trouble shooting failed runs.

Just my $0.02 worth for someone wholly unfamiliar with the software to get going with as few headaches as possible.

[westerman]

I should have clarified that I use the "command line only" which can be installed by a non-root user. Ditto with command line + GUI. A full install with Command Line + GUI + AutoExport does require root access.

A good sysadmin will carefully control access to the system and will not allow an install program to be run as root without assurances that the program will not stomp all over the file system. My sysadmin is very careful and questioned why I needed the "full install" at which point I realized that a lower level install would be good enough. YMMV.

My problem with the ini files -- aside from them changing between bioscope versions -- was how any given run had to have parameters changed in multiple ini files. I finally got the ini files arranged so that I could change one file and the setup would ripple down through the other files. With the GUI the ini files are more defined.

[guo]

Dear all,
Thank you for your comments ---it can be a learning process for me! But my results are still the same, which stay like this:
$ /home/guo/bioscope_root/bioscope/bin/bioscope.sh –l /file13/guo/bioscope/log/mapping/workflow_mapping.log /file13/guo/examples/demos/mapping/mapping.ini
+/home/guo/bioscope_root/bioscope/bin+
+/home/guo/bioscope_root/bioscope+
2011 Sep 22 20:51:21, 894 HKT INFO [main] PluginJobManager:107 - >>>> START of PluginJobManager >>>> date=2011-09-22 20:51:21.879 HKT
2011 Sep 22 20:51:21, 905 HKT INFO [main] PluginJobManager:110 - Bioscope version: bioscope-v1.3-rBS131_55029_20101119113500…
I checked and double checked the .ini/.plan files (global.ini+mapping.ini for the above run),everything is in the full path of directory…… bioscope is re-installed by the administer…..the configuration is with 10 nodes and 8 cores……JMS is running….. the bioscope queue should be OK (assured by my system administer)…
One thing is the directory structure, I have to install the example folder outside of my HOME because of space limit, does this matter? Which folder should I submit the job? Again does it matter? ….
According to your comments, things I am not sure (or do not understand) are ------- If the “bioscope.conf” in /bioscope/etc/conf presents the default settings, should I replace it with the “bioscope.conf” generated by installation, and run update_bioscope.sh? how about the configure_bioscope.sh?
Many thanks for your time and patience!
Guo

[Milan Radovich]

You may have already done this, but is your JDK version at least JDK 1.6.0_12?

[guo]

You may have already done this, but is your JDK version at least JDK 1.6.0_12?

Thanks, Milan. The problem now is fixed. It happened at the installation, we did not use the correct user name, like 'guo', in my case... seems funny, but suddenly things turned to be fine, when we changed the name.