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Problem in get_tool_shed_status_for_installed_repository()
by Simon Guest 14 Oct '13

14 Oct '13

Hi Greg, I think this would be yours. I've recently upgraded to the development branch, and I'm getting HTTP 404 errors from the new function get_tool_shed_status_for_installed_repository(). What gets logged is this: tool_shed.util.shed_util_common ERROR 2013-10-14 09:44:17,448 Error attempting to get tool shed status for installed repository emboss_datatypes: HTTP Error 404: Not Found Traceback (most recent call last): File "/home/galaxy-dev/galaxy/lib/tool_shed/util/shed_util_common.py", line 1226, in get_tool_shed_status_for_installed_repository encoded_tool_shed_status_dict = common_util.tool_shed_get( app, tool_shed_url, url ) File "/home/galaxy-dev/galaxy/lib/tool_shed/util/common_util.py", line 191, in tool_shed_get response = urlopener.open( uri ) File "/usr/lib64/python2.6/urllib2.py", line 397, in open response = meth(req, response) File "/usr/lib64/python2.6/urllib2.py", line 510, in http_response 'http', request, response, code, msg, hdrs) File "/usr/lib64/python2.6/urllib2.py", line 435, in error return self._call_chain(*args) File "/usr/lib64/python2.6/urllib2.py", line 369, in _call_chain result = func(*args) File "/usr/lib64/python2.6/urllib2.py", line 518, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 404: Not Found When I enhanced the log output like this: log.exception( "Error attempting to get tool shed status for installed repository %s (%s) (%s): %s" % ( str( repository.name ), str(tool_shed_url), str(url), str( e ) ) ) I saw this in the log: tool_shed.util.shed_util_common ERROR 2013-10-14 09:55:26,584 Error attempting to get tool shed status for installed repository emboss_datatypes (http://toolshed.g2.bx.psu.edu) (http://toolshed.g2.bx.psu.edu/repository/status_for_installed_repository?na…) HTTP Error 404: Not Found It occurs to me that the main toolshed may not be running with this feature enabled yet, and perhaps I should just ignore this error for now? (I'd like to be running the development branch for other features it gives me. Alternatively, I could think about back-porting the features I really need to stable, but that sounds like more work than I have time for.) When's the next stable release planned to be released, and what should I expect to be in it? cheers, Simon

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SeqPrep wrapper?
by Lionel Guy 14 Oct '13

14 Oct '13

Hi, I'm interested in a wrapper for SeqPrep: https://github.com/jstjohn/SeqPrep Anyone preparing one/aware of someone preparing one? Otherwise I'll put one together. From its description: "SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap." Cheers, Lionel Lionel Guy Uppsala University

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questions on test_admin_features
by 分析流 13 Oct '13

13 Oct '13

Hi, all: I'm setting a local galaxy, everything is fine (galaxy can run and I can also login) but always got a lot of errors in functional.test_admin_features for example, test_015_login_after_password_reset Exception: ... Traceback (most recent call last): File "/usr/lib64/python2.6/unittest.py", line 279, in run testMethod() File "/home/galaxy/main/galaxy-dist/test/functional/test_admin_features.py", line 89, in test_015_login_after_password_reset raise AssertionError( 'No DefaultHistoryPermissions were created for history id %d when it was created' % latest_history.id ) AssertionError: No DefaultHistoryPermissions were created for history id 119 when it was created -------------------- >> begin captured stdout << --------------------- form 'login' contains the following controls ( note the values ) --------------------- >> end captured stdout << ---------------------- am I missing something in configuration? Thanks a lot! kind rgds, Ray.

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Data Integration - Gencode Partition tool
by Hans-philipp Brachvogel 12 Oct '13

12 Oct '13

Hello! This is more or less a repost of (several) previously unanswered questions. Sadly it seems that one does generally not recieve an answer to this topic: http://lists.bx.psu.edu/pipermail/galaxy-user/2011-October/003400.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007088.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-October/011478.html So how do I properly set up the Gencode Partition tool (or the ENCODE tools)? Another thing: the official galaxy instance seems to have the same problem: The tool Gencode Partition returns the error: "Error loading partitioning dataset." which I also experience when using the the testing-bed file from galaxy-dist/test-data/encode_1.bed I suppose the encode_1.bed file is not the problem, right? Another thing is the helptext defined in the XML: it points to http://genome.imim.es/gencode/wiki/index.php/Collecting_Feature_Sets_from_A… The wiki is actually closed by password... Best, Phil

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Trouble viewing History from a particular laptop
by Jennifer Jackson 11 Oct '13

11 Oct '13

Hi Olivia, Our development team suggests checking the paster.log, plus, if applicable, proxy server logs. From what we know, this kind of issue generally indicate a firewall issue, but without more information, it is difficult to diagnose. Please keep replies on this mailing list instead (is the one for local install questions). Thanks! Jen Galaxy team On 10/9/13 2:31 PM, Olivia Choudhury wrote: > Hello, > > I am a graduate student in the University of Notre Dame. I have > installed a personal instance of Galaxy and have been developing tools > there as a part of my research. > > Everything worked well on my laptop until recently, when I could not > view the 'History' panel, no matter which browser (Firefox, Chrome, > Safari) I used on my laptop (Windows 7 OS). Everything works > absolutely fine and I can view 'History' when I am using a desktop or > any other laptop. > > I have checked this across different operating systems and also > ensured that no changes were made with the Firewall setup of my laptop. > > I have attached a print screen of what the Galaxy page looks like. > > It would be great if I could get some help with this. > > > Thanks a lot in advance, > Olivia > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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cleanup_datasets.py with postgresql 8.1
by Jennifer Jackson 11 Oct '13

11 Oct '13

Posting to galaxy-dev(a)bx.psu.edu to give the question better exposure to the development community. Please _remove the galaxy-user(a)bx.psu.edu mailing list from all replies_ - we want to avoid double posts. > 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 On 9/26/13 7:29 AM, Malcolm Tobias wrote: > > All, > > My understanding is that the cleanup_datasets.py under > scripts/cleanup_datasets should be compatible with 'older' versions of > postgresql. I'm running 8.1 under CentOS 5. When I attempt to run the > scripts, it fails to clean any data sets. From the logs, I'm noticing > messages like: > > database_connection contains an unknown SQLAlchemy database dialect: > postgresql > > In my universe_wsgi.ini I've defined the database_connection as: > > database_connection = postgresql://galaxy:********@localhost:5432/galaxydb > > and am confident it's working as Galaxy works fine, other than this > problem with deleting older datasets. > > The pgcleanup.py script isn't an option, as it requires postgresql > >=9.1. I noticed yet another version of cleanup_datasets.py under cron > which looks like it might be compatible with postgres, but am leary of > trying it as I'm not sure what it means by "1: database directory to > clean". I'm not sure what directory to point this to, nor am I > confident that just deleting data from the directory is the safest thing. > > Any suggestions on how to proceed? > > Thanks! > > Malcolm > > -- > > Malcolm Tobias > > 314.362.1594 > > > > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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Solenopsis invicta genome
by patrick.joye＠unil.ch 11 Oct '13

11 Oct '13

Hello, I'm working in the university of Lausanne. We are currently working with fire ants, Solenopsis invicta. I was wondering if that would possible to upload Solenopsis invicta's genome on the Galaxy platform, which could be very useful to us and certainly to other people. Thank you ! Patrick Joye

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masthead and history lost when embedding Galaxy in iframe
by Andy Saurin 11 Oct '13

11 Oct '13

Hi all, I really can't understand why this should be, but in recent versions of Galaxy if you have a simple html page with an iframe embedding Galaxy, you loose the masthead (no login, workflow etc) and the history panel no longer works. eg (newer Galaxy Versions) <iframe src="https://galaxy.cbio.mskcc.org/" width="800px" height="600px"></iframe> <iframe src="https://galaxy.cbio.mskcc.org/" width="800px" height="600px"></iframe> You can see the problems, whereas older versions of galaxy show no problems: <iframe src="http://galaxy.berkeleybop.org:8080/" width="800px" height="600px"></iframe> What could be causing this so that I can try to make amends? Thanks Andy

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Error when running paster directly
by Renato Alves 11 Oct '13

11 Oct '13

Hi everyone, When trying to adapt the init script for debian machines (provided in contrib/) I started playing with paster directly. I was trying to get some sort of help or list of commands/params that can be passed but instead I was presented with the following output: $ python ./scripts/paster.py Usage: ./scripts/paster.py COMMAND Command 'help' not known (you may need to run setup.py egg_info) Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/galaxy/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/galaxy/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/galaxy/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 367, in run commands = get_commands().items() NameError: global name 'get_commands' is not defined After inspection of the file, the get_commands function doesn't seem to be defined nor imported. I'm not sure how to proceed at this point. Thanks, Renato

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Unicode in tool stderr crashing galaxy?
by Guest, Simon 11 Oct '13

11 Oct '13

My optimism was short lived. I think I've hit a galaxy bug in Unicode processing. Having managed to get the deseq tool not to crash galaxy in the sqlalchemy layer, I now get a crash when clicking on the info->stderr for the tool output dataset, probably because it contains Unicode. Here's the traceback from paster.log: ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 47124) Traceback (most recent call last): File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__ self.handle() File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request self.wsgi_execute() File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 150, in wsgi_write_chunk self.wfile.write(chunk) File "/usr/lib64/python2.6/socket.py", line 316, in write data = str(data) # XXX Should really reject non-string non-buffers UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 169: ordinal not in range(128) ---------------------------------------- I don't know where to look to find the actual stderr output. Any pointers? Is this actually a galaxy bug now? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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