galaxy-dev October 2011

galaxy-dev@lists.galaxyproject.org

90 participants
149 discussions

Local installation
by Mattia Chiesa 25 Oct '11

25 Oct '11

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 Il Tuo 5 per Mille a favore della Ricerca del Centro Cardiologico Monzino va dritto al cuore. 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. 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 (1 3 0 5 5 6 4 0 1 5 8) ed apponi la Tua firma. Questo messaggio � riservato esclusivamente ai destinatari indicati e pu� contenere informazioni di pertinenza o propriet� del Cardiologico Monzino o comunque di carattere privato. Qualora lo riceveste per errore, Vi preghiamo di darcene immediata comunicazione e successivamente di eliminarlo. E' vietato qualunque altro uso del messaggio difforme da quanto indicato. This message is for the designated recipient only and may contain privileged, proprietary, or otherwise private information. If you have received it in error, please notify the sender immediately and delete the original. Any other use of the email by you is prohibited.

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Galaxy Main public instance: data and job quotas
by Jennifer Jackson 25 Oct '11

25 Oct '11

Galaxy Main public instance: data and job quotas October 25, 2011 Dear Galaxy User, Thank you very much for using our free and open public resource. Galaxy has become extremely popular and as a result many people rely on it daily for their analysis needs. Previously our service had no restrictions on usage, which is not sustainable in the long term. To continue providing our open service in a fair manner, we are now implementing quotas at the public Galaxy Main instance http://usegalaxy.org (http://main.g2.bx.psu.edu). The Main quotas are: Data - 250Gb for registered users (with a Galaxy account) - 5Gb for unregistered users Jobs - 8 concurrent jobs running simultaneously (all users) For more details please see: Galaxy Main Wiki http://galaxyproject.org/wiki/Main Data management: accounting and disk quotas http://galaxyproject.org/wiki/Admin/Disk%20Quotas Managing Datasets in Galaxy http://galaxyproject.org/wiki/Learn/Managing%20Datasets#Actions For those users with current account disk usage over the quota limit, we will be implementing a step-down program over the next several weeks. Details for that program will be emailed to those users directly. If you find that you require additional resources, please consider the alternative Galaxy options: http://galaxyproject.org/wiki/Big%20Picture/Choices Thanks for using Galaxy! -- The Galaxy team http://usegalaxy.org http://getgalaxy.org http://galaxyproject.org

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Broad IGV
by Chorny, Ilya 24 Oct '11

24 Oct '11

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>

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FTP UPLOAD
by alessandro albiero 24 Oct '11

24 Oct '11

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 ********************************

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Importing Historys in other Galaxy instances
by Stefanie Ververs 24 Oct '11

24 Oct '11

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

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Problem uploading sorted BAM files
by Stephen Eacker 24 Oct '11

24 Oct '11

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

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Database configuration
by Luciano Cosme 24 Oct '11

24 Oct '11

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

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Re: [galaxy-dev] FW: one error while installing galaxy
by Nate Coraor 24 Oct '11

24 Oct '11

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/

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Re: [galaxy-dev] Few possible galaxy bugs ?
by Peter Cock 24 Oct '11

24 Oct '11

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

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upload error in the local instance of galaxy
by Amit Anand 24 Oct '11

24 Oct '11

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 Information in this email is confidential and may also be privileged. It is intended solely for the person to whom it is addressed. If you are not the intended recipient, please notify the sender, and please delete the message and any other record of it from your system immediately.

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galaxy-dev October 2011