Local installation
by Mattia Chiesa
Hi
I'm Chiesa Mattia and I write from an hospital in Milan (ITALY).
I
want to install Galaxy locally on a CentOS platform. I read in your
documentation that Python 2.5/2.6 is required but for some function also
Python
2.4 (installed in our CentOS) is okay.What are these
functions?
Thanks a lot
Mattia
<br><strong><span style='font-size:11.0pt;line-height:115%;font-family:Arial'>Il Tuo 5 per Mille a favore della Ricerca del Centro Cardiologico Monzino va dritto al cuore.</span></strong><br><br><span style='font-size:9.0pt;line-height:115%;font-family:Arial'>Tutti coloro che presentano il modello Unico, il modello 730 o piu semplicemente che ricevono dal proprio datore di lavoro il modello CUD, hanno la facolta di scegliere la destinazione del proprio 5 per mille.</span><br><span style='font-size:9.0pt;line-height:115%;font-family:Arial'>Nella casella riservata al <a href='http://www.cardiologicomonzino.it/Ricerca/Pages/campagna2010.aspx'>Finanziamento agli Enti della Ricerca Sanitaria</a> inserisci il codice fiscale del CCM (</span><span style='font-size:11.0pt;font-family:Arial;color:red'><b>1 3 0 5 5 6 4 0 1 5 8</span></b></span><span style='font-size:9.0pt;line-height:115%;font-family:Arial;color:black'>) ed apponi la Tua firma.</span></p>
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10 years, 7 months
Broad IGV
by Chorny, Ilya
I saw some posts and a commit which allows one to use broad IGV within galaxy but I do not see a tool, a link, or an option. Can someone explain how to set that up?
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>
10 years, 7 months
FTP UPLOAD
by alessandro albiero
Dear all,
I've a question about FTP upload of data.
The data uploaded via ftp are placed in the directory ftp_upload_dir defined
in universe_wgsi.uni
After the uploading, when a user select the data to import in its history,
galaxy copy the file in the dir file_path (defined in universe_wgsi.uni).
In this manner we have two copy of the same file, and with NGS data this not
the best solution...
I try to set the ftp_upload_dir and the file_path with the same path
but galaxy copy the file in a dir called 000. In my ftp_upload_dir
/ file_path so I have:
- user1(a)mail.com
- user2(a)mail.com
- 000
How can I avoid this duplication ?
All the Best
Alessandro
--
******************************
Alessandro Albiero
Bioinformatics Lab
CRIBI-Padua University
Viale G. Colombo, 3
35121 Padova-Italy
http://genomics.cribi.unipd.it
http://genomics.cribi.unipd.it/index.php/User:Albiero
Phone. +39. 049 827-6165
Fax. +39. 049 827-6159
********************************
10 years, 7 months
Importing Historys in other Galaxy instances
by Stefanie Ververs
Hi everybody,
I got another question concerning our own Galaxy instance.
We are trying to import Histories from the public Galaxy server via
"Export to file" (in the public-Galaxy-account), saving the export-Link
and "Import from File" in the account on our local system.
But the histories never show up there. As I read in some older mails,
you need to be logged in the source account - I was, I checked that.
Am I correct that it's possible to "copy" histories between different
Galaxy instances at all? (I assume because it's the only case that makes
sense to me..)
We thought it might depend on some Apache configuration, but didn't
figure it out yet.
Maybe someone's got some ideas :-)
Regards,
Steffi
10 years, 7 months
Problem uploading sorted BAM files
by Stephen Eacker
Hello,
I'm trying to upload a 600MB BAM file to my local instance of Galaxy but the upload fails. I tried to follow a thread on this topic archived on osdir.com but could not find if the issue was resolved. My BAM file has been previously been sorted and indexed which I think is the root of the problem. Advice?
thanks,
Steve
Stephen Eacker, Ph.D.
Postdoctoral Fellow
Dawson Lab
Institute for Cell Engineering
Johns Hopkins Medical Institute
(443) 287-5605
seacker1(a)jhmi.edu
10 years, 7 months
Database configuration
by Luciano Cosme
Hi,
I am sorry about the trivial questions. I am following this guide
http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP to set up a ftp
server to upload data to my local instance of galaxy. I am getting a error
when I am configuring the database server:
postgres@aedes:~$ createuser -SDR galaxyftp
postgres@aedes:~$ psql galaxydb
psql (9.1.1)
Type "help" for help.
galaxydb=# ALTER ROLE galaxyftp PASSWORD 'dbpassword';
ALTER ROLE
galaxydb=# GRANT SELECT ON galaxy_user TO galaxyftp;
ERROR: relation "galaxy_user" does not exist
galaxydb=#
It might be something pretty simple, but I am new to it and any help will be
appreciated. I create the user galaxy_user already.
Thank you.
Luciano
10 years, 7 months
Re: [galaxy-dev] FW: one error while installing galaxy
by Nate Coraor
Li, Jilong (MU-Student) wrote:
> Hi,
>
> When I installed galaxy, one error message appeared, which said that
>
> ImportError: No module named distutils.util
> Fetch failed.
>
> Could you tell me how to solve this problem?
> Thank you very much!
Hi Jilong,
Since this is a question regarding a local installation, I've moved it
over to the galaxy-dev list.
Could you try the following:
% unset PYTHONPATH
% python ./scripts/fetch_eggs.py
And then try to start Galaxy again?
--nate
> ___________________________________________________________
> 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/
10 years, 7 months
Re: [galaxy-dev] Few possible galaxy bugs ?
by Peter Cock
On Mon, Oct 24, 2011 at 3:55 PM, michael burrell (TOC)
<michael.burrell(a)nbi.ac.uk> wrote:
> Good afternoon Peter,
>
> Thank you for your rapid response,
>
> My understanding is that this tool was installed locally from the tool shed, unfortunately I do not know if it was working before the update was performed.
>
> Other tools installed from the tool shed do not seem to report errors, would you have any advice on resolving the small nlstradamus issue that is reported here?
>
> Thanks again for the information.
>
> Michael.
I'm hoping Greg can give some clues. This part suggests Galaxy is
trying to read the text readme file as if it were XML:
galaxy.tools ERROR 2011-10-20 13:18:47,722 error reading tool from
path: toolshed/nlstradamus/tools/protein_analysis/nlstradamus.txt
...
ExpatError: syntax error: line 1, column 0
Peter
10 years, 7 months
upload error in the local instance of galaxy
by Amit Anand
Hi,
I have just installed a local instance of galaxy. Though I am not too familiar with unix, I preferred a local instance because of large amount of data I have to process. However, I am unable to upload a file more that 2 GB in size, the error log is pased below
127.0.0.1 - - [19/Oct/2011:15:06:08 +0800] "POST /tool_runner/index HTTP/1.1" 500 - "http://127.0.0.1:8080/tool_runner?tool_id=upload1" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:6.0.2) Gecko/20100101 Firefox/6.0.2"
Debug at: http://127.0.0.1:8080/_debug/view/1319007854
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 61099)
Traceback (most recent call last):
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 617, in __init__
self.handle()
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle
BaseHTTPRequestHandler.handle(self)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request
self.wsgi_execute()
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 287, in wsgi_execute
self.wsgi_start_response)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/urlmap.py", line 202, in __call__
return app(environ, start_response)
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py", line 21, in __call__
return self.app( environ, start_response )
File "/Users/amit/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg/paste/deploy/config.py", line 164, in __call__
app_iter = self.application(environ, start_response)
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py", line 68, in __call__
return self.application(environ, replacement_start_response)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 226, in __call__
return self.respond(environ, start_response)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py", line 399, in respond
if self.xmlhttp_key in req.params:
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 900, in params
params = self.str_params
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST
keep_blank_values=True)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 510, in __init__
self.read_single()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 647, in read_single
self.read_lines()
File "/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/base.py", line 253, in read_lines
self.read_lines_to_outerboundary()
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/cgi.py", line 697, in read_lines_to_outerboundary
line = self.fp.readline(1<<16)
File "/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 467, in readline
data = self.file.readline(self.length - self._consumed)
File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/socket.py", line 409, in readline
bline = buf.readline(size)
OverflowError: long int too large to convert to int
Please help me to fix this, the python version is 2.6.6. Thank you.
Sincerely,
Amit,
Germline biology group
Temasek Life Sciences Laboratory
Singapore
--
Amit Anand
Germ Line Biology Group
Temasek Life Sciences Laboratory
1, Research Link
National University of Singapore
Singapore, 117604
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10 years, 7 months
