purging deleted datasets
by Erick Antezana
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
13 years, 1 month
Using mysql instead of sqlite
by Erick Antezana
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
13 years, 3 months
Experience with Loading NGS data on standalone instance of galaxy
by Abhishek Pratap
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/
13 years, 3 months
various import dir's
by Erick Antezana
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
13 years, 4 months
'MySQL server has gone away'
by Pieter Neerincx
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
------------------------------------------------------------
13 years, 5 months
[Fwd: Re: Fresh install has wrong layout]
by Chris Cole
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#Apacheconfigurati...
>>>
>>> --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
13 years, 6 months
Galaxy, NGS Data, and SAMtools?
by Dave Clements
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
13 years, 6 months
fasta_to_tabular.py slowness
by Rasmus Ory Nielsen
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 ) )
13 years, 6 months
DB migration scripts?
by Erick Antezana
Hi,
is there any migration script, bundeled with Galaxy, to assist in the
sqlite to mysql migration?
thanks,
Erick
13 years, 6 months
Re: [galaxy-user] Request for " Find cluster intervals" tool
by Anton Nekrutenko
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
13 years, 6 months
