October 2013 - galaxy-dev - lists.galaxyproject.org

about the sqlalchemy-migrate
by ngsflow＠hygenomics.com 15 Oct '13

15 Oct '13

hi,all: 1. when I started the galaxy daemon. In the paster.log has a warning.who can help me. url= http://code.google.com/p/sqlalchemy-migrate/ 2. missing file. 3.What should I do about it? 4.What should I do about it? ngsflow(a)hygenomics.com

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How to specify the availability zone when using cloudman?
by Carlos Borroto 15 Oct '13

15 Oct '13

Hi, I'm getting this error when trying to restart a previously used cluster: "InvalidVolume.ZoneMismatchThe volume '' is not in the same availability zone as instance" I did a search and I could only find this previous email in galaxy-user: http://lists.bx.psu.edu/pipermail/galaxy-user/2012-January/003946.html Which while confirming I should make sure to match the new instance zone with previous volumes zone, it does not say how to do it. Thanks, Carlos

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launching CloudMan 2.0 on AWS
by Vipin TS 14 Oct '13

14 Oct '13

Hi dev-team, I am trying to launch cloudman on AWS us-east-1a and I am getting the message *All cluster services started; the cluster is ready for use. (2013-10-14 19:45:52)* I am seeing some error message in the log. * 19:05:33 - Master starting* * 19:05:35 - Could not find service class matching userData service entry: PSS* * 19:05:35 - Completed the initial cluster startup process. This is a new cluster; waiting to configure the type.* * 19:06:11 - Migration service prerequisites OK; starting the service* * 19:06:11 - SGE service prerequisites OK; starting the service* * 19:06:26 - Setting up SGE...* * 19:06:40 - HTCondor service prerequisites OK; starting the service* * 19:06:48 - Hadoop service prerequisites OK; starting the service* * 19:07:04 - Done adding Hadoop service; service running.* * 19:08:13 - Initializing 'Galaxy' cluster type. Please wait...* * 19:08:14 - Error creating volume: EC2ResponseError: 400 Bad Request VolumeLimitExceededMaximum number of active volumes bytes, 20, exceeded.66659429-b0dd-4f88-b763-36fd9232d3c4* * 19:08:17 - Adding volume vol-f9c4728e (FS object for galaxy)...* * 19:08:42 - Successfully grew file system FS object for galaxy* * 19:08:42 - Successfully mounted file system /mnt/galaxy from /dev/xvdf* It seems that the galaxyIndices filesytem is not mounted to the instance. Also I am not able to start the postgres or Galaxy service through cloudman interface, both says that Cannot find the service. Please find the attached image. I think I am missing the galaxyIndices volume from the image,. any idea about the failure to launch the instance. Thanks, Vipin http://galaxy.cbio.mskcc.org

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Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud
by Stanislas Werfel 14 Oct '13

14 Oct '13

Dear all, I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman distribution (ami-118bfc78). The instatiated Galaxy however does not contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. Although the wrappers are there in the tools directory, when I access it through ssh. I've also installed Bowtie2 manually on the server and the command bowtie2 does get recognized. How cat I get these two to run on the Galaxy instance? Thanks for your help. Best Stanislas

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AttributeError: type object 'InvalidJobException' has no attribute 'name'
by Adhemar 14 Oct '13

14 Oct '13

Hi, After the last update I'm getting the following error. The job is submitted to SGE e executed, but galaxy doesn't get the result and keeps showing the job is executing (yellow box). Any clues? Thanks, Adhemar galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception checking active jobs Traceback (most recent call last): File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/__init__.py", line 362, in monitor self.check_watched_items() File "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/drmaa.py", line 217, in check_watched_items log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) AttributeError: type object 'InvalidJobException' has no attribute 'name'

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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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