[galaxy-dev] Importing Historys in other Galaxy instances
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Exporting histories through API
Hello there As the subject hints, I am trying to export histories through the API. Doing it through the web interface is a breeze, but has it been implemented in the API yet? I could not find anything about it in the examples or by searching the web/this list. I am planning to only use Galaxy through the API to import my data and run some workflows on it, and then export the results. Preferably specific files from the history, but a bundled history like the one you get from the web interface 'Export history' would be ok as well. Has anyone done something like this, and can point me in the right direction? :) Mvh Martin Dahlö --- Bioinformatic support martin.da...@scilifelab.uu.se +46 18 611 59 59 +46 706 70 79 55 http://www.scilifelab.uu.se/ http://www.uppnex.uu.se --- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Data Retention Policies
On Oct 24, 2011, at 2:57 AM, Peter Cock wrote: On Mon, Oct 24, 2011 at 4:53 AM, John Chilton chil...@msi.umn.edu wrote: Hello All, This is more of a general policy question. The head of our Research Informatics Support Systems group here at the University of Minnesota wants to know how other institutions are handling the large amount of data generated by next generation sequencing facilities and processed by local Galaxy instances. Specifically, I think she is interested in what sort of data retention policies institutions have in place - for instance how long do you store data, what sort of quotas do you put in place, what sort of backups do you have in place, etc Any comments would be appreciated. Thanks for your time, -John Might be worth asking on the bioinformatics core facilities mailing list too, I know some of the folk there use Galaxy in their institutes: http://open-bio.org/mailman/listinfo/bioinfo-core Peter We're in the (very long, drawn-out) process of integrating much of our local bioinformatics resources to also deal with this problem. We have a general plan in place, including adding automated tape backup and a number of other features on the analysis end (storage for fast I/O, etc), but I'm interested in hearing more from others on this. chris ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Few possible galaxy bugs ?
On Mon, Oct 24, 2011 at 3:55 PM, michael burrell (TOC) michael.burr...@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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper?
Any more thought on how to accomplish this without my current hack? Ideally it would be great if this feature could become part of galaxy-central. This is a feature that we would really like to implement so that our reports can link to the output files. Thanks, Ilya -Original Message- From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Friday, October 21, 2011 9:47 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: RE: [galaxy-dev] FW: how do I pass the URL of the input and output files to my tool wrapper? Excerpts from Chorny, Ilya's message of 2011-10-21 01:51:03 +: I get the following error from routes AttributeError: 'thread._local' object has no attribute 'mapper' Okay, what I suspected. This is a product of the fact that job running is decoupled from the web frontend. The job runner doesn't necessarily live in the same process or even on the same machine as the web interface. You could have multiple web interfaces serving different base urls feeding one job runner. I don't have any simple answer to this. You could try to initialize route's mapper in the job runner, but I think this would be a big mistake. Instead you probably want to capture the URL somehow when the job is created. I need to think about it some more. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] upload error in the local instance of galaxy
Brad Langhorst wrote:
On 10/19/11 3:09 AM, Amit Anand a...@tll.org.sg wrote:
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
Hi anand:
It¹s not possible to upoad such big files.
You need to use FTP or local file import methods to do that.
See:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
?highlight=%28import%29
Brad
You probably also need to set:
debug = False
use_interactive = False
In universe_wsgi.ini
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/httpserv
er.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/httpserv
er.py, line 432, in handle
BaseHTTPRequestHandler.handle(self)
File
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/BaseHTTPServe
r.py, line 329, in handle
self.handle_one_request()
File
/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
er.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/httpserv
er.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.p
y, line 202, in __call__
return app(environ, start_response)
File
/Users/amit/galaxy-python/galaxy-dist/lib/galaxy/web/framework/middleware/xfo
rwardedhost.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/tra
nslogger.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/e
valexception/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/e
valexception/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(116)
File
/Users/amit/galaxy-python/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserv
er.py, line 467, in readline
data = self.file.readline(self.length - self._consumed)
File
Re: [galaxy-dev] FW: one error while installing galaxy
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/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Job output not returned from cluster
Joseph Hargitai wrote: Nate, this error is intermittent. You resubmit the same job twice or three time and then it works. Once we are over the midterm exams - which use galaxy - we will try to switch the filesystem from autofs to hard mount. We suspect this to be the issue. Ah, I suspect this is attribute caching in NFS. Try mounting with the option 'noac' and see if it solves the problem. Could we suppress e and o SGE style to resolve this issue, or Galaxy wants the o? The filename is unimportant, but I doubt it's the cause. Do you have an idea about the url build for galaxy - ucsc page return when the url is :8080/galaxy and not just /galaxy? Not off the top of my head. I have this message marked, I'll take a look as soon as I have time. --nate thanks, joe From: Nate Coraor [n...@bx.psu.edu] Sent: Friday, October 21, 2011 10:26 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from cluster Joseph Hargitai wrote: Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. Hi Joe, This error occurs when the job's standard output and error files are not found where Galaxy expects them, namely: cluster_files_directory/job_id.o cluster_files_directory/job_id.e Please check your queueing system to make sure it can correctly deliver these back from the execution hosts to the specified filesystem. --nate thanks, joe ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem uploading sorted BAM files
Stephen Eacker wrote: 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? Hi Steve, Are there any errors reported, either in the web interface or the Galaxy server output? --nate thanks, Steve Stephen Eacker, Ph.D. Postdoctoral Fellow Dawson Lab Institute for Cell Engineering Johns Hopkins Medical Institute (443) 287-5605 seack...@jhmi.edu ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Broad IGV
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: icho...@illumina.commailto:icho...@illumina.com Website: www.illumina.comhttp://www.illumina.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Broad IGV
Hi Ilya, In datatypes_conf.xml, under the bam datatype uncomment out the display application for igv/bam (display file=igv/bam.xml /). Links will then appear for bam history items. Thanks for using Galaxy, Dan On Oct 24, 2011, at 5:50 PM, Chorny, Ilya wrote: 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: icho...@illumina.com Website: www.illumina.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
