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database migration error 79->80 (NameError: name 'BigInteger' is not defined)
by Edward Kirton 01 Sep '11

01 Sep '11

hi, we are getting the following error migrating from 79 to 80. curiously, my own galaxy didn't have this problem, but another developer here was getting this error. i moved him from sqlite to postgres but that didn't help. thanks for any assistance, ed Migrating 79 -> 80... galaxy.model.migrate.check INFO 2011-08-31 13:15:31,446 Traceback (most recent call last): File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", line 67, in create_or_verify_database migrate_to_current_version( engine, db_schema ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", line 125, in migrate_to_current_version schema.runchange( ver, change, changeset.step ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 100, in run File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 112, in _func File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 108, in module File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 65, in verify_module File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/util/importpath.py", line 12, in import_path File "lib/galaxy/model/migrate/versions/0080_quota_tables.py", line 29, in <module> Column( "bytes", BigInteger ), NameError: name 'BigInteger' is not defined

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Question about data size
by Jennifer Jackson 31 Aug '11

31 Aug '11

Hi Doug, I am going to forward your question to the galaxy-dev mailing list so that the development community can offer feedback based on their experience. Best, Jen Galaxy team On 8/15/11 9:47 AM, Douglas Hinerfeld wrote: > HI There, > I am trying to get my head around how much data is generated when > analyzing Illumina HiSeq data in Galaxy. I understand that it totally > depends on what type of analytical pipelines are used. From our own > usage, we are seeing the generation of about 30 bytes of data generated > per base of sequence. I don’t know if you have any data on this that can > be shared, but I am just trying to get a sense if this is similar to > other’s experience. > Thanks, > Doug -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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[API] managing histories
by Louise-Amélie Schmitt 31 Aug '11

31 Aug '11

Hello everyone, I'm currently trying to automate data loading and pre-processing through Galaxy's API, and I will need to delete and share histories at some point. I know the API is still very new but is there a way to do that by any chance? Thanks, L-A

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Re: [galaxy-dev] [galaxy-user] install tools on cluster
by Nate Coraor 31 Aug '11

31 Aug '11

Wei,Xintao wrote: > Hi, > > I am learning how to install and configure Galaxy on our computer cluster. Many third party tools, for example, bowtie, samtools, R and so on, have to be installed and configured in order to install galaxy. Do I have to convert the third party tools to MPI version in order to run the tools on a computer cluster? Or do I just install the "regular" version of the tools on the "shared" folder of our cluster? Hi Xintao, I've moved this question over to the dev list since it concerns a local installation. You don't need to convert them to MPI, they run as serial jobs on a single node. Note that you can specify the number of cores to use in the tool's config file, which you'll want to set for the nodes you're running them on. --nate > > Thank you! > > Xintao > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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Backup strategy
by Oleksandr Moskalenko 31 Aug '11

31 Aug '11

Hello, Considering the fact that a galaxy instance can grow to be quite large I wonder what Galaxy backup strategies and implementations other people actually have in use and are happy with. Thanks, Alex

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bug or feature :)
by Bossers, Alex 31 Aug '11

31 Aug '11

In our local instance (central version) up to changeset (June 28th) I noticed in the admin panel to manage jobs some odd behaviour; When I set the update Jobs cutoff on 10 seconds and press refresh.... the item below (administrative Job Lock) is also activated and new jobs are locked. Is that a planned feature, a bug or is something wrong in our local instance. Another refresh toggles it back to normal. Alex

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Wrapper generator.
by J. F. J. Laros 31 Aug '11

31 Aug '11

Dear, I need to add a number of tools to my local Galaxy installation, but the size of the wrappers I've seen keep me from writing one. Are there wrapper generators to make this task easier? If not, I might want to make one. A possible implementation I'm considering is to first make a (WSDL) description of any command line tool (using soaplab2 for example) and by making a general wrapper builder that takes WSDL as input. Does something similar already exist and if not, does this idea sound okay? With kind regards, Jeroen. -- Jeroen F. J. Laros - J.F.J.Laros(a)lumc.nl

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August 30, 2011 Galaxy Development News Brief
by Jennifer Jackson 31 Aug '11

31 Aug '11

August 30, 2011 Galaxy Development News Brief http://galaxyproject.org/wiki/News%20Briefs/2011_08_30 Source: http://getgalaxy.org new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 949e4f5fa03a What's New ISMB/ECCB, BOSC, and 3DSIG 2011 Slides Recent Publications GalaxyProject.org Wiki Tool Shed Upcoming Events Updated & Improved Data Tools Visualization (Trackster) Workflows API Source Quotas Bug Fixes

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Tools requiring java can't find java
by Chorny, Ilya 30 Aug '11

30 Aug '11

This is probably a question for our sys admin but when I run tools such as GATK I get an error java command not found. I can execute java from the command line and it works. Further I can grab the drmaa submission script (ie galaxy_job_id.sh) and qsub it from the command line and it finds JAVA. Any thoughts? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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[API] Get the hashed dataset id within Galaxy
by Louise-Amélie Schmitt 30 Aug '11

30 Aug '11

Hi, I would need to make a tool that can get the API dataset id out of the input dataset of the tool, how can I do that?

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