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Currently, if I attempt to abandon or stop a running build I see the following failure:
```
ogriffit@GGMS /opt/gms/XFOKC32/sw/genome (gms-pub)> genome model build stop 350dfa8932f643fd966132559bb6d09…
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Alignment jobs immediately enter a 'pending' state. bjobs -l reports the following:
PENDING REASONS:
Not enough job slot(s);
Not enough job slot(s);
The resource request looks like this:
```
4 Pro…
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For some reason, RNA-seq jobs run on the standalone GMS are using only 1 CPU during the alignment step (instead of 12). The lsf requested resources for the job look like this:
Requested Resources
…
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Latest attempt to install sGMS in a VM is failing the first time it tries to run code that uses Genome:
```
Module::Runtime version v0.14.0 required--this is only version v0.11.0 at /opt/gms/B518B12/…
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At some point in the gms-pub branch of gms-core repository, BWA commands were overridden to use 20x cpus. This was probably done because we were not able to correctly parse available cpus from openla…
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Some work has started here:
Genome/InstrumentData/Command/Export/Samplesheet.pm
Need to decide how to handle the actual BAM files, not just the metadata associated with instrument data, samples, libr…
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No idea what this is about, or whether it is consequential. Don't think I have seen it before either.
ogriffit@GGMS ~> genome model build start 2891230328 2891230330
'models' may require verificatio…
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We want the following ultimate setup:
4 disks total:
- 1 VMDK for the OS, '/' mounted on a partition 'sda1' of 'sda' device within the VM. Vagrant does this for us when we fire up Ubuntu precise. …
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Getting the following error when I try to run make vm from a fresh checkout now:
The following packages have unmet dependencies:
genome-snapshot-deps : Depends: genome-snapshot-deps-r
(=2013.09.06…