Dear all,
Has anyone tried running Galaxy on Ubuntu 14.04?
I’m trying a test setup on two virtual machines (worker+master) with a SLURM
queue. Getting in strange problems when jobs finish, the master hangs,
completely unresponsive with CPU at 100% (as reported by virt-manager, not by
top).
Hi Dave,
Can you tell me any more about this failed tool dependency error:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
Installation errors
Tool dependencies
TypeNameVersion
MIRA package 4.0
Error
File
I should probably mention that the data filesystem is NFS, exported by the
master from /mnt/galaxy/data and mounted on the worker. No separate fileserver.
Master is the one that hangs.
cheers,
—
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden
On 07
I'll try to keep this short! I'm wondering why on a fresh install of galaxy
via a setup script into a python virtualenv, my custom toolshed tool's .loc
files don't seem to be loading, i.e. the tool's tool_data_table_conf.xml file
isn't loading. All the other parts of the tool (and other
Hello List,
I'm writing a tool_dependencies.xml file for a python package.
It defines an action type=setup_virtualenv, and when I install it to
my galaxy from the test shed it is actually installed into
~/environments, and the tool definition is set up correctly.
This package includes a
One further piece of the mystery I see now:
The View Data tables Registry shows my tool's loc files, but has odd stuff
for Tool data path and Missing index file columns, for example:
blast_reporting_fields [tab]
So I see this now in main.log:
galaxy.tools.data WARNING 2014-05-07 16:40:29,613 Line 3 in tool data table
'blast_reporting_fields' is invalid (HINT: 'TAB' characters must be used to
separate fields):
length numeric int 1 1 1
Alignment length
The
Well Galaxians, I have to eat humble pie, kind of. Mismatches between the
tool's tool_data_table_conf.xml and the actual tabular data were responsible
for the disappearing act, which log rather indirectly alluded to. Something
that didn't show itself on the dev server.
I'll push for some
