July 2009 - galaxy-user - lists.galaxyproject.org

purging deleted datasets
by Erick Antezana 17 Dec '09

17 Dec '09

Hi, how can I purge my deleted datasets that were imported so that I could clean a bit my disk? I saw they are under database/files/000/* thanks, Erick

3 6

Using mysql instead of sqlite
by Erick Antezana 04 Nov '09

04 Nov '09

Hello, I would like to use MySQL instead of sqlite to store my data. I coudn't find on the Galaxy web site a HOWTO or some guidelines to do it. I only found some lines that might need to be changed/enabled in the universe_wsgi.ini file: #database_file = database/universe.sqlite database_connection = mysql:///galaxy #database_engine_option_echo = true #database_engine_option_echo_pool = true #database_engine_option_pool_size = 10 #database_engine_option_max_overflow = 20 Could you point out to some doc or briefly describe what I need to do in order to go for mysql? Are there any plans to support other DBMS's (like Oracle for instance)? thanks, Erick

5 15

Experience with Loading NGS data on standalone instance of galaxy
by Abhishek Pratap 04 Nov '09

04 Nov '09

Hi All I recently came to know about NGS analysis on galaxy during ISMB. Getting excited I tried couple of things basically to play with it. Few comments : I may have interepretted something described below in a wrong way. My apologies before hand. On a standalone installation of galaxy while I was trying to explore one FASTQ(sequence) file. It takes considerable (> 20 min) for a fastq file to get uploaded (2 GB). I am not sure what is the rationale behind that. Ideally I think there should be no need to upload such heavy files into the workspace. They could actually be used straight away by the path specified. Also is there any way to access the scripts for analysis on the command line. I know this undermines the main aim of working with galaxy but rite now I am concerned about the performance/time. I will be happy to discuss more about this in case you have some comments/questions for me. Best, -Abhi ----------------------------- Abhishek Pratap Bioinformatics Software Engineer Institute for Genome Sciences School of Medicine, Univ of Maryland 801, W. Baltimore Street, Baltimore, MD 21209 Ph: (+1)-410-706-2296 www.igs.umaryland.edu/

8 26

various import dir's
by Erick Antezana 15 Sep '09

15 Sep '09

Hi, how can I defined various library import directories within the "universe_wsgi.ini" by using the "library_import_dir" ? same question for "user_library_import_dir"? thanks, Erick

5 5

'MySQL server has gone away'
by Pieter Neerincx 19 Aug '09

19 Aug '09

Hi, Every morning when I come back to my lab and login to Galaxy I get the error below. I think it's the 'MySQL server has gone away' part that is the real cruel-pitand simply clicking refresh is enough to 'fix' the problem... This is not specifically a Galaxy problem. It's probably the result of caching connections and I have seen this before when I was using Perl modules to access MySQL databases. I guess this can be solved by fiddling with sqlalchemy settings maybe even in a Galaxy config file, but I'm a Python noob. If anyone has seen this before and knows how to properly fix it, please let me know. Cheers, Pi URL: http://tadpole/galaxy/ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/WebError-0.8a-py2.4.egg/weberror/evalexception/ middleware.py', line 364 in respond File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/debug/prints.py', line 97 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/wsgilib.py', line 539 in intercept_output File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Beaker-0.5-py2.4.egg/beaker/session.py', line 103 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/recursive.py', line 80 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/middleware/remoteuser.py', line 102 in __call__ return self.app( environ, start_response ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/Paste-1.5.1-py2.4.egg/paste/httpexceptions.py', line 632 in __call__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/base.py', line 100 in __call__ trans = self.transaction_factory( environ ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 109 in <lambda> self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 149 in __init__ self.__ensure_valid_session( session_cookie ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 277 in __ensure_valid_session user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/lib/galaxy/web/ framework/__init__.py', line 361 in __get_or_create_remote_user user = self .app .model .User .filter( self.app.model.User.table.c.email==remote_user_email ).first() File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 909 in first File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 938 in __iter__ File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/query.py', line 941 in _execute_and_instances File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/orm/session.py', line 628 in execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 844 in execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 895 in execute_clauseelement File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 907 in _execute_compiled File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 916 in __execute_raw File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 960 in _cursor_execute File '/mnt/npc01d01/prog/galaxy-2009-07-08-3bbb2d2caa5f/eggs/py2.4- noplatform/SQLAlchemy-0.4.7p1-py2.4.egg/sqlalchemy/engine/base.py', line 942 in _handle_dbapi_exception OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_user.id AS galaxy_user_id, galaxy_user.create_time AS galaxy_user_create_time, galaxy_user.update_time AS galaxy_user_update_time, galaxy_user.email AS galaxy_user_email, galaxy_user.password AS galaxy_user_password, galaxy_user.external AS galaxy_user_external, galaxy_user.deleted AS galaxy_user_deleted, galaxy_user.purged AS galaxy_user_purged \nFROM galaxy_user \nWHERE galaxy_user.email = %s ORDER BY galaxy_user.id \n LIMIT 0, 1' ['P.B.T.Neerincx(a)uu.nl'] ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx(a)gmail.com skype: pieter.online ------------------------------------------------------------

2 3

[Fwd: Re: Fresh install has wrong layout]
by Chris Cole 30 Jul '09

30 Jul '09

Just realised I'd not sent this to the list. Whoops! This is still broken, anyone have any ideas? Cheers, Chris -------- Original Message -------- Subject: Re: [galaxy-user] Fresh install has wrong layout Date: Tue, 21 Jul 2009 10:47:50 +0100 From: Chris Cole <chris(a)compbio.dundee.ac.uk> Organisation: University of Dundee To: Nate Coraor <nate(a)bx.psu.edu> References: <4A4E147C.6010107(a)compbio.dundee.ac.uk> <4A4E1506.5030609(a)bx.psu.edu> <4A4E1716.2070800(a)compbio.dundee.ac.uk> <4A52AFFA.5020102(a)bx.psu.edu> Hi Nate, Sorry for not replying earlier, I've been on holiday. Attached should be my universe_wsgi.ini for the updated server. (The file has a .txt extension to avoid sending blockage). I've used the same settings (where applicable) for my currently working svn version 1686. Chris Nate Coraor wrote: > Chris, > > Could you send us your universe_wsgi.ini? We haven't seen this happen > without a proxy before. > > --nate > > Chris Cole wrote: >> Hi Nate, >> >> Nope. There's no proxy configured. The only things I changed in the HTTP >> config part of the universe_wsgi.ini are the host and the port. >> Cheers, >> >> Chris >> >> Nate Coraor wrote: >>> Hi Chris, >>> >>> It sounds like you maybe be running through a proxy, away from the >>> server root, without the proxy-prefix option set in universe_wsgi.ini? >>> If so, have a look at the documentation here: >>> >>> http://g2.trac.bx.psu.edu/wiki/HowToInstall/ApacheProxy#Apacheconfiguration… >>> >>> --nate >>> >>> Chris Cole wrote: >>>> Hi, >>>> >>>> I've been using the subversion version of Galaxy for a while, but now I >>>> want to update to the latest mercurial release. >>>> >>>> I installed it in a new location as per the wiki and set-up the SGE >>>> settings as per my previous install and all the tests pass. It launches >>>> fine, but when viewing the website the frames seem to be off-by-one. >>>> i.e., the 'Tools' frame is empty except for "This link may not be >>>> followed from within Galaxy.", the tools are in the middle window and >>>> the 'History' frame has general information. >>>> >>>> I can't see any errors in the paster.log file, so where can I look to >>>> sort out this error? >>>> Thanks, >>>> >>>> Chris >>>> _______________________________________________ >>>> galaxy-user mailing list >>>> galaxy-user(a)bx.psu.edu >>>> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user >> > -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096 -- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris(a)compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096

1 0

Galaxy, NGS Data, and SAMtools?
by Dave Clements 24 Jul '09

24 Jul '09

Hello all, I just scanned the recent thread started by Abhi Pratap, titled "Experience with Loading NGS data on standalone instance of galaxy" I didn't see any mention of the SAMtools in that thread. SAMtools is a platform neutral set of formats and programs for next generations sequence data. See http://samtools.sourceforge.net/ for more. Has the Galaxy team considered adding support for SAMtools formats? It might be a way to deal with all the NGS platforms with a single set of code. Dave C. -- Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting

2 1

fasta_to_tabular.py slowness
by Rasmus Ory Nielsen 23 Jul '09

23 Jul '09

Hi Galaxy Team, I've found that fasta_to_tabular.py is very slow with big sequences, e.g. ~4 minutes for a single 5MB sequence. The patch below makes the running time go from minutes to seconds for such a sequence. Mind you, this is my first line of python, so there may be a smarter way. Best regards, Rasmus Ory Nielsen --- fasta_to_tabular.py.orig 2009-07-18 16:25:50.896487000 +0200 +++ fasta_to_tabular.py 2009-07-18 17:22:49.544611000 +0200 @@ -34,7 +34,7 @@ fasta_seq = '' else: if line: - fasta_seq = "%s%s" % ( fasta_seq, line ) + fasta_seq += line if fasta_seq: out.write( "%s\t%s\n" %( fasta_title[ 1:keep_first ], fasta_seq ) )

5 11

DB migration scripts?
by Erick Antezana 22 Jul '09

22 Jul '09

Hi, is there any migration script, bundeled with Galaxy, to assist in the sqlite to mysql migration? thanks, Erick

2 1

Re: [galaxy-user] Request for " Find cluster intervals" tool
by Anton Nekrutenko 22 Jul '09

22 Jul '09

Charu: Please, direct these types of requests to mailing lists rather than to specific developers. The problem with adding the space of **** if that it will completely break the format definition, so this is not a good idea. If you want to enumerate clusters I would propose the following workflow: 1. Identify clusters (dataset 1) 2. Merge them using the "Operate on Genomic Intervals -> Merge" (dataset 2) 3. Add identifiers using the "Text manipulation -> Add column tool"(dataset 3) 4. Join your cluster (dataset 1) with dataset 3 using "operate on Genomic Intervals -> Join" This should solve your issue. Let me know if you have trouble. Thanks, anton galaxy team On Jul 21, 2009, at 6:41 PM, Charu Gupta Kumar wrote: > Dear Dr. Nekrutenko, > > I was wondering if it would be possible to make a small change to > the "Find > cluster intervals, output grouped by clusters" tool (Find cluster > intervals; > output grouped by clusters is part of "Operate on Genomic Intervals"): > > Ques.) Would it be possible to add a newline (or ***) after every > cluster > grouping, so users know when one cluster starts and another ends? It > would > be most helpful in figuring out the cluster demarcations. > > Thanks so much, > > Best regards, > > Charu > Charu Gupta Kumar, Ph.D. > > ****************** > > For example, > > chr6_random 3253 3745 AA577868 0 + 3 > chr6_random 3663 3896 BI789243 0 + 1 > chr6_random 3663 4054 BM351966 0 + 1 > chr6_random 3663 7171 CK903338 0 + 3 > chr6_random 3847 7979 CK903339 0 - 4 > chr6_random 3878 7963 BI962749 0 - 4 > chr6_random 4062 7581 BM352279 0 - 4 > chr6_random 4610 5058 AA828152 0 + 2 > chr6_random 5243 5460 BM353279 0 - 2 > chr6_random 5255 5403 BM314916 0 + 1 > (space or ****** here) > chr6_random 23107 23724 BU657553 0 - 1 > chr6_random 23489 27653 BF507618 0 - 2 > chr6_random 27113 27791 BI086568 0 + 9 > chr6_random 70525 75802 BC064362 0 + 2 > chr6_random 70514 73863 DA960595 0 + 3 > chr6_random 70525 71258 BM470002 0 + 12 > > > Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

1 0