Ubuntu Install errors

[data-vis]

Dear Authors,

I installed gms on fresh ubuntu 12.4

We had to manually add Paths variables to .bashrc

GENOME_SYS_ID=cat /etc/genome/sysid
GENOME_HOME="/opt/gms/$GENOME_SYS_ID"
PATH=/opt/openlava-2.2/bin/:/opt/gms/YOX9E130/sw/genome/bin/:$PATH
PERL5LIB=/opt/gms/YOX9E130/sw/genome/lib/perl/

Still not able to workout the genome command

ubuntu@analysis:~$ genome
Use of inherited AUTOLOAD for non-method UR::Util::use_package_optimistically() is deprecated at /opt/gms/YOX9E130/sw/genome/lib/perl/Genome/Site.pm line 27.
Can't locate object method "use_package_optimistically" via package "UR::Util" at /opt/gms/YOX9E130/sw/genome/lib/perl//Genome.pm line 24
BEGIN failed--compilation aborted at /opt/gms/YOX9E130/sw/genome/lib/perl/Genome/Site.pm line 49.
Compilation failed in require at /opt/gms/YOX9E130/sw/genome/lib/perl//Genome.pm line 24.
Compilation failed in require at (eval 3) line 2.
BEGIN failed--compilation aborted at (eval 3) line 2.
BEGIN failed--compilation aborted at /opt/gms/YOX9E130/sw/genome/bin/genome line 23.

ubuntu@analysis:~$ bhosts
HOST_NAME STATUS JL/U MAX NJOBS RUN SSUSP USUSP RSV
analysis ok - 16 0 0 0 0 0

ubuntu@analysis:~$ lsload
HOST_NAME status r15s r1m r15m ut pg ls it tmp swp mem
analysis ok 0.0 0.0 0.0 0% 0.0 1 0 1731G 0M 62Gn

[sakoht]

Rather than hand-edit your .bashrc, you should just source /etc/genome.conf.

The make process should have made a .bash_aliases file in your home directory that does that, along with other cosmetic stuff you may or may not want. You can source that instead in your .bashrc/.bash_profile, if you like, or go directly to the underlying conf.

Did you see any errors during the install process?

[data-vis]

Thank you, it worked well.
I did not notice any errors and also do not have a .bash_aliases in home directory. I had to run make with sudo. Without sudo it just wouldn't accept my ubuntu password even after resetting it multiple time.

[data-vis]

Can I look for these errors somewhere before putting ask you for help?

ubuntu@analysis:~/gms$ ./setup/prime-system.pl --help

This system appears to already be primed (i.e. /opt/gms/primed exists). There is no need to do this step again

ubuntu@analysis:~/gms$ genome model build start "name='hcc1395-normal-refalign-exome'"
'models' may require verification...
Resolving parameter 'models' from command argument 'name='hcc1395-normal-refalign-exome''... found 1
Trying to start #1: hcc1395-normal-refalign-exome (2891377978)...
WARNING: Could not copy model input hcc1395-normal-refalign-exome (2891377978) genotype_microarray: hcc1395-normal-snparray (2891230330) to build fa4c833031c24e86aa1d0566933692af of hcc1395-normal-refalign-exome of model hcc1395-normal-refalign-exome (2891377978) because Could not resolve a build of model hcc1395-normal-snparray (2891230330) at /opt/gms/YOX9E130/sw/genome/lib/perl/Genome/Model/Build.pm line 469.
Build IDs: fa4c833031c24e86aa1d0566933692af

[sakoht]

I had to run make with sudo. Without sudo it just wouldn't accept my ubuntu password even after resetting it multiple time.

Not sure what will happen with that.

If your install has already run once as root, you may have a lot of files with root permissions that need something less exclusive. And you don't want the genome sys config bash scripts in root's home dir.

My suggestion: Start clean, and make a non-root, non-ubuntu user, that can sudo. Run a fresh install as that.

[data-vis]

Start clean, and make a non-root, non-ubuntu user, that can sudo

Thank you, It worked well. Now, running the demo data. When I click on the models (all 16) in web browser it's giving a red colour font error "We're sorry, but something went wrong"

[data-vis]

hcc1395-somatic-exome, have been running for 3 days. Should i restart it?

hcc1395-tumor-refalign-exome and hcc1395-normal-refalign-exome were finished in 30 min. Thank you very much in advance.

[malachig]

It might be that you ran out of processing slots and are in a locked state where new jobs are trying to start but there are none available. Trying abandoning the build and starting a new one. If this problem persists you may need to tweak the openlava configuration.