September 2012 - galaxy-dev - lists.galaxyproject.org

Instantiate Galaxy on AWS
by Ravvaz, Kourosh 25 Sep '12

25 Sep '12

Dear Sir/Madam, I just started to instantiate a Galaxy instance on the AWS. I have followed your instructions on the following page: http://wiki.g2.bx.psu.edu/CloudMan http://wiki.g2.bx.psu.edu/CloudMan/AWS/GettingStarted At the end of step 2, I faced a problem which resulted in the following error: The Galaxy Cloud Console is not running. It may take a few moments to start after your EC2 instance has become available, or you may not have provided the correct user data when configuring and launching the instance from the AWS Management Console. Please refer to the documentation for more information. If you did enter the correct user data, you may be able to reboot this EC2 instance to solve the problem. So, I rebooted the instance and then since the problem was not resolved I terminated the instance and created another instance. I did so a few times. However, it did not help. I have reviewed my AWS credentials and also the master instance (AMI: ami-da58aab3, Name: 861460482541/galaxy-cloudman-2011-03-22). Every thing looks fine. Would you please help me fix this? Regards, Kourosh

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problem installing blast_datatypes manually
by Liisa Koski 25 Sep '12

25 Sep '12

Hello, I followed the instructions below to manually install the blast_datatypes: Manual Installation =================== Normally you would install this via the Galaxy ToolShed, which would move the provided blast.py file into a suitable location and process the datatypes_conf.xml entry to be combined with your local configuration. However, if you really want to this should work for a manual install. Add the following line to the datatypes_conf.xml file in the Galaxy main folder: <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking the blast.py file provided in this tar-ball. Finally add 'import blast' near the start of file lib/galaxy/datatypes/registry.py (after the other import lines). ========================= I restarted my local Galaxy instance but still get this error. WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml' Any help would be much appreciated. Thanks, Liisa

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Can't edit Galaxy Workflow _ElementInterface instance has no attribute 'render'
by Liisa Koski 25 Sep '12

25 Sep '12

Hello, After updating to the Sept. 07 distribution I am having problems editing an existing workflow. Server error URL: http:galaxy_url/workflow/load_workflow?id=ba751ee0539fff04&_=1348501448807 Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:69 in decorator >> return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.web.controllers.workflow:735 in load_workflow >> 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:262 in get_tooltip >> return self.tool.help.render( static_path=static_path ) AttributeError: _ElementInterface instance has no attribute 'render' Any help would be much appreciated. Thanks in advance, Liisa

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dynamically send jobs to second cluster on high load
by Geert Vandeweyer 24 Sep '12

24 Sep '12

Hi, The admin pages state that it is possible to specify multiple clusters in the universe file. Currently, we are investigating if we can couple the university HPC platform to galaxy, to handle usage peaks. It would be ideal if the job manager would check the load of the dedicated cluster (eg queue length) and send jobs to the second cluster when load is above a threshold. Does such an approach exists already, or will it become available in the near future? As far as I understand, it is now only possible to specify which jobs run on which cluster, without dynamic switching? Best regards, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

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When will the API allow setting of parameters (not inputs) from the API
by Thon Deboer 24 Sep '12

24 Sep '12

Hi, One of the biggest hurdles for the implementation in our institute is the inability of Galaxy API to set parameters at run time. You can only seem to set inputs, but not parameters... Is there any ETA on when this will be available? Is this even a priority? Thanks! Regards, Thon de Boer, Ph.D. Bioinformatics Guru +1-650-799-6839 thondeboer(a)me.com LinkedIn Profile

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python egg cache exists error
by Jorrit Boekel 24 Sep '12

24 Sep '12

Dear list, I am running galaxy-dist on Amazon EC2 through Cloudman, and am using the enable_tasked_jobs to run jobs in parallel. Yes, I know it's not recommended in production. My jobs usually get split in 72 parts, and sometimes (but not always, maybe in 30-50% of cases), errors are returned concerning the python egg cache, usually: [Errno 17] File exists: '/home/galaxy/.python-eggs' or something like [Errno 17] File exists: '/home/galaxy/.python-eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg-tmp' The errors arise AFAIK from when scripts/extract_dataset_part.py is run. I am guessing that the tmp python egg dir is created for every task of the mentioned 72, that they sometimes coincide and that this leads to an error. I would like to solve this problem, but before doing so, I'd like to know if someone else has already fixed it in a galaxy-central changeset. cheers, jorrit

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The user creation and login script can be injected with executable javascript in Galaxy
by Hanfei Sun 24 Sep '12

24 Sep '12

Hello Galaxy-team, A galaxy instance is being hold on our server. But last week, an expert in security makes some tests on our server. He warned us that the user creation and login script can be injected with executable javascript in Galaxy, which may make our server vulnerable. He gives us a report of 3 pages (other issues including Non-SSL Password and cookie of Galaxy). We don't know whether it's serious and whether we need to fix these issues immediately. Is Galaxy going to update for issues? Or we need to modify them ourselves? Any suggestion is appreciated. Thanks! -- Hanfei Sun Sent with Sparrow (http://www.sparrowmailapp.com/?sig)

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Galaxy not recording return codes (error levels)
by Peter Cock 21 Sep '12

21 Sep '12

Dear all, Is there a plan to record the return code (error level) in the Galaxy Job history, along with the stdout and stderr strings? I would find this very useful - especially for situations where a job is killed (e.g. by the OS) and there is no indication of why it died (stderr is empty). Thanks, Peter

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Re: [galaxy-dev] Using an unique database for tow differents versions of Galaxy
by James Taylor 21 Sep '12

21 Sep '12

Definitely not. And please keep replies on the list. -- jt On Fri, Sep 21, 2012 at 1:50 PM, Chebbi Mohamed Amine <chebbimamine(a)gmail.com> wrote: > Yes the two instances are of two different versions. So if I understand well > there is no mean to do it like this ? > Thanks > > > 2012/9/21 James Taylor <james(a)jamestaylor.org> >> >> If the two different Galaxy instances are different *versions* of >> Galaxy, this is unlikely to work out well. >> >> -- jt >> >> >> On Fri, Sep 21, 2012 at 11:59 AM, Chebbi Mohamed Amine >> <chebbimamine(a)gmail.com> wrote: >> > Hello Galaxy-team! >> > >> > I installed recently two differents versions of Galaxy and I would like >> > to >> > use the same database for the two instances without loosing data >> > (histories, >> > workflows etc..). >> > >> > Thank you in advance >> > Amine >> > >> > ___________________________________________________________ >> > 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/ > >

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Using an unique database for tow differents versions of Galaxy
by Chebbi Mohamed Amine 21 Sep '12

21 Sep '12

Hello Galaxy-team! I installed recently two differents versions of Galaxy and I would like to use the same database for the two instances without loosing data (histories, workflows etc..). Thank you in advance Amine

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