Hans-Rudolf Hotz wrote:
> Hi Colin
>
>
> Please keep all replies on the list by using "reply all"
>
>
> You are aware of the 'download' button (ie the disk icon), aren't-you?
>
> Unless, you have a log-in requiorement for your galaxy server, you can
> also use this url to copy the data to a different server with 'wget'.
>
> Or you try to find out the dataset number (eg by setting up 'reports' or
> just by looking at the filesystem) and you do an 'scp' to your other server
Thanks Hans,
FWIW, I have a crummy little script I use to translate encoded/decoded
dataset IDs and return datasets' disk paths, attached. Maybe others
will find this useful.
--nate
>
> Regards, Hans
>
>
>
>
> On 06/29/2011 11:58 PM, colin molter wrote:
> >Hi Hans,
> >just one more small galaxy question.
> >I finished the whole process of transforming the data using galaxy. Now i
> >would like to get these data into my server's filesystem. Something exactly
> >opposite to the adding of datafile to a datalibrary would be ideal.
> >(so getting a dataset from the history to the filesystem).
> >
> >thx for your time,
> >regards,
> >colin
> >
> >2011/6/29 colin molter<colin.mol...@gmail.com>
> >
> >>it finished! and results seems perfect.
> >>it is just very very slow: nearly 10 hours for 25Gb.
> >>
> >>it seems that in future version of illumina preprocessed data, there will
> >>be no longer need of the groomer.
> >>thx
> >>colin.
> >>
> >>
> >>2011/6/29 Hans-Rudolf Hotz<h...@fmi.ch>
> >>
> >>>
> >>>
> >>>On 06/28/2011 07:06 PM, colin molter wrote:
> >>>
> >>>>hi hans,
> >>>>you are right.
> >>>>it seems that even if i stopped galaxy
> >>>>(i just stopped the run.sh command)
> >>>>
> >>>>i still have a job running:
> >>>>root 10441 97.0 0.0 77496 1772 pts/6 R 11:59 402:48 python
> >>>>/opt/galaxy-central/tools/**fastq/fastq_groomer.py
> >>>>/fs1/GenomicsData/ERP0005
> >>>>
> >>>>it seems that the transformation of a fastq file is taking a lot of time
> >>>>(it
> >>>>uses 100%of cpu since 7hours).
> >>>>does it sound normal?
> >>>>
> >>>>
> >>>I am not very familiar with 'fastq_groomer.py' and without knowing the
> >>>size of your fasta file, it is impossible to tell.
> >>>
> >>>Have you tried a subset of your fasta file? May be your data is corrupt
> >>>resulting in an endless loop?
> >>>
> >>>
> >>>Hans
> >>>
> >>>
> >>>
> >>> i think i have better to kill that job and to try another way.
> >>>>
> >>>>i stopped the job and it works
> >>>>thx.
> >>>>
> >>>>
> >>>>2011/6/28 Hans-Rudolf Hotz<h...@fmi.ch>
> >>>>
> >>>> Hi Colin
> >>>>>
> >>>>>
> >>>>> I launched a big job on my local galaxy server (for which I am admin).
> >>>>>The
> >>>>>
> >>>>>>job was to put local dir in the datalist.
> >>>>>>It took too long and i wanted to stop it .... but how?? i failed to
> >>>>>>find a
> >>>>>>solution.
> >>>>>>
> >>>>>>
> >>>>>go to the admin view -> 'Manage jobs' and there you can kill individual
> >>>>>jobs.
> >>>>>
> >>>>>
> >>>>> To stop the job i thought that stopping the galaxy running instance
> >>>>>could
> >>>>>
> >>>>>>make it. (AM I RIGHT?)
> >>>>>>
> >>>>>>
> >>>>>possible, but sounds like an 'overkill' to me. I would first try the
> >>>>>'soft'
> >>>>>method described above....and use this only as a last resort.
> >>>>>
> >>>>>
> >>>>> Unfortunately, i failed to restart galaxy. I have the following error:
> >>>>>
> >>>>>>
> >>>>>>
> >>>>>> are you sure you have killed the galaxy process? Since this part of
> >>>>>the
> >>>>>error message tells me that Galaxy (or another service) is still using
> >>>>>the
> >>>>>port number.
> >>>>>
> >>>>>
> >>>>> socket.error: (98, 'Address already in use')
> >>>>>>
> >>>>>
> >>>>>
> >>>>>How did you stop galaxy?
> >>>>>
> >>>>>
> >>>>>
> >>>>>Regards, Hans
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>>
> >>
> >>
> >>--
> >>Colin Molter
> >>University of Brussels - InSilico Team - http://insilico.ulb.ac.be/
> >>
> >>
> >
> >
> ___________________________________________________________
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#!/usr/bin/env python
import os, sys
from ConfigParser import ConfigParser
from optparse import OptionParser
parser = OptionParser()
parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' )
parser.add_option( '-e', '--encode-id', dest='encode_id', help='Encode an ID' )
parser.add_option( '-d', '--decode-id', dest='decode_id', help='Decode an ID' )
parser.add_option( '--hda', dest='hda_id', help='Display HistoryDatasetAssociation info' )
parser.add_option( '--ldda', dest='ldda_id', help='Display LibraryDatasetDatasetAssociation info' )
( options, args ) = parser.parse_args()
try:
assert options.encode_id or options.decode_id or options.hda_id or options.ldda_id
except:
parser.print_help()
sys.exit( 1 )
options.config = os.path.abspath( options.config )
os.chdir( os.path.dirname( options.config ) )
sys.path.append( 'lib' )
from galaxy import eggs
import pkg_resources
config = ConfigParser( dict( file_path = 'database/files',
id_secret = 'USING THE DEFAULT IS NOT SECURE!',
database_connection = 'sqlite:///database/universe.sqlite?isolation_level=IMMEDIATE' ) )
config.read( os.path.basename( options.config ) )
from galaxy.web import security
from galaxy.model import mapping
helper = security.SecurityHelper( id_secret = config.get( 'app:main', 'id_secret' ) )
model = mapping.init( config.get( 'app:main', 'file_path' ), config.get( 'app:main', 'database_connection' ), create_tables = False )
if options.encode_id:
print 'Encoded "%s": %s' % ( options.encode_id, helper.encode_id( options.encode_id ) )
if options.decode_id:
print 'Decoded "%s": %s' % ( options.decode_id, helper.decode_id( options.decode_id ) )
if options.hda_id:
try:
hda_id = int( options.hda_id )
except:
hda_id = int( helper.decode_id( options.hda_id ) )
hda = model.context.current.query( model.HistoryDatasetAssociation ).get( hda_id )
print 'HDA "%s" is Dataset "%s" at: %s' % ( hda.id, hda.dataset.id, hda.file_name )
if options.ldda_id:
try:
ldda_id = int( options.ldda_id )
except:
ldda_id = int( helper.decode_id( options.ldda_id ) )
ldda = model.context.current.query( model.HistoryDatasetAssociation ).get( ldda_id )
print 'LDDA "%s" is Dataset "%s" at: %s' % ( ldda.id, ldda.dataset.id, ldda.file_name )
___________________________________________________________
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