- galaxy-user - lists.galaxyproject.org

error when creating a user
by Paul Rigor (prigor＠uci) 04 Aug '09

04 Aug '09

Hi, Has anyone encountered this error when attempting to create a new user? Thanks, paul URL: http://localhost/user/create File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/debug/prints.py', line 98 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Beaker-0.5-py2.6.egg/beaker/session.py', line 103 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/recursive.py', line 80 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Paste-1.5.1-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/controllers/user.py', line 178 in create .add_input( "checkbox","Subscribe To Mailing List","subscribe", value='subscribe' ) ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 557 in show_form return self.fill_template( template, form=form, header=header ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 566 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/web/framework/__init__.py', line 577 in fill_template_mako return template.render( **data ) File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/template.py', line 114 in render File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 287 in _render File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 304 in _render_context File '/home/prigor/projects/galaxy/genomics/galaxy_dist/eggs/py2.6-noplatform/Mako-0.1.10-py2.6.egg/mako/runtime.py', line 337 in _exec_template File '/home/prigor/projects/galaxy/genomics/galaxy_dist/database/compiled_templates/ base.mako.py', line 33 in render_body context.write(unicode(next.body())) AttributeError: 'builtin_function_or_method' object has no attribute 'body' -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor

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error even starting up galaxy
by Paul Rigor (prigor＠uci) 03 Aug '09

03 Aug '09

Hi gang, I've setup galaxy to run before. But this time around, the server will not start. The setup is fairly straightforward though I'm using python 2.6. Below is the error message stack. I've made some modifications to the configuration, but just pathing and db stuff. I've even run a python shell to import the new module which works fine. Any suggestions will be really helpful, thanks! Paul Traceback (most recent call last): File "./scripts/paster.py", line 16, in <module> from galaxy import eggs File "/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/galaxy/__init__.py", line 5, in <module> __import__( "pkg_resources" ).declare_namespace( __name__ ) File "/home/prigor/projects/galaxy/genomics/galaxy_dist/lib/pkg_resources.py", line 16, in <module> import sys, os, zipimport, time, re, imp, new ImportError: No module named new (2.6.2)04:42 PM 16807 prigor@localhost~/projects/galaxy/genomics/galaxy_dist $ python /home/prigor/projects/galaxy/genomics/galaxy_dist/lib/pkg_resources.py -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor

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[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

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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

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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 ) )

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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

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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

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Fwd: Request for " Find cluster intervals" tool
by Anton Nekrutenko 22 Jul '09

22 Jul '09

Begin forwarded message: > From: "Charu Gupta Kumar" <cgkumar(a)illinois.edu> > Date: July 21, 2009 6:41:59 PM EDT > To: "'Anton Nekrutenko'" <anton(a)bx.psu.edu> > Subject: Request for " Find cluster intervals" tool > > 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

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Problems with history
by SHAUN WEBB 16 Jul '09

16 Jul '09

I have just updated galaxy with the latest mercurial change sets and I am having a few problems with the history. The history is not automatically refreshing so new jobs appear to still be queuing/running. Also, I can't permanently delete an item from the history. It remains with the message "This item has been deleted" even if I try to delete it again. Is this a feature in the latest update. Is anyone else having these problems? Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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library usage screencast?
by Erick Antezana 16 Jul '09

16 Jul '09

Hi, is there any screencast or documentation that could be used to learn more about the library usage? (from the users and admin points of view. In the case of the admin, I guess the user_library_import_dir and library_import_dir settings need only be changed?) thanks, Erick

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