galaxy-user May 2010

galaxy-user@lists.galaxyproject.org

41 participants
44 discussions

identification of regions
by research pal 05 May '10

05 May '10

Dear Galaxy, First of all let me thank you people for the effort that you are involved in to help the bench scientists world over. I have the ChIP data from ENCODE and I want to see from which part i.e. Exon,Intron or intergenic regions of the human genome they are derived from.In this case can the tools available at galaxy or genome browser help me to reduce my manual efforts ? warm regards, Amit.

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Easy linkage to user dataset files
by Matthew Vaughn 04 May '10

04 May '10

Dear Galactic Overlords, I'd like to be able to provide external access via HTTP GET-able URL to individual data files that are generated in the course of Galaxy analysis. For example, say a user wanted to import her data in Galaxy, do some basic manipulation and then download the resulting data file into another environment using curl or wget... If the user is not authenticated into the Galaxy server (ie is a guest), and she copies the link from a data set in her history by right clicking on the 'Save' icon, she gets something like this: http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval and this URL is retrievable via curl -O "http://main.g2.bx.psu.edu/datasets/259589cb863ac26a/display?to_ext=interval" resulting in a file. However, if the user is coming from an authenticated environment, the link will fail with a Permissions Error from Galaxy. Presumably, this is because the server is checking for presence of a cookie that is set during user authentication. Short of sniffing the authentication token and passing it using curl/wget along with the request (and this will fail when the token expires), is there any way to accomplish what I am asking? Is there a way to provide user credentials via the URL string perhaps? Thanks, Matt == Matthew W. Vaughn, Ph.D. Scientific Lead, iPlant Collaborative Research Assistant Professor Cold Spring Harbor Laboratory 1 Bungtown Road Williams #5 Cold Spring Harbor, NY 11724 USA web: http://hispaniola.cshl.edu/ web: http://www.iplantcollaborative.org/ tel: (516) 367-8808 cell: (516) 353-7055 google-talk: matt.vaughn(a)gmail.com

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Changing fastq to fastqillumina fails
by Ryan Golhar 04 May '10

04 May '10

I've uploaded a compressed (gzip) fastq file into galaxy. The file is recognized as fastq. When I try to run the FASTQ Summary Statistics program on the uploaded file, I don't see the file listed in the drop-down box. I then tried to change the type of the file from fastq to fastqillumina and I get the following error: ⇝ TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given) URL: http://genomes.umdnj.edu/galaxy/library_common/ldda_edit_info?library_id=22… File '/opt/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/opt/galaxy_dist/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) TypeError: ldda_edit_info() takes exactly 6 non-keyword arguments (5 given) -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

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Re: [galaxy-user] [galaxy-dev] Configuring MySQL for Galaxy (and vice versa)
by Jeremy Goecks 04 May '10

04 May '10

Hi Bastien, Please make sure to cc the galaxy-user and galaxy-dev lists as they help your questions reach a wider audience. In fact, I'm sure there are people on these lists that have more DB knowledge than myself. That said, you're spot on in your thinking. Galaxy uses a single database (galaxy, in your case), so you can setup a "Galaxy" mysql user to have rights only on that DB; specifying localhost provides another layer of security as well. Best, J. On May 3, 2010, at 11:08 AM, Chevreux, Bastien wrote: >> From: Jeremy Goecks [mailto:jgoecks@gmail.com] On Behalf Of Jeremy Goecks >> You can specify a MySQL username and password in the MySQL URL, e.g. >> mysql://username:password@localhost:3306/galaxy?unix_socket=/var/run/ >> mysqld/mysqld.sock > > Hello Jeremy, > > thank you very much for that, works like a charm. > > Coming to my next question: how should I setup the user / user rights / databases / tables etc. in MySQL? > > Yes, I could create a user and then do a > > grant all privileges on *.* to someusr@localhost > > and I think that that Galaxy will then create everything by itself. However, on the long term I feel that this might be ... um ... a security risk should MySQL also host other things than just a Galaxy DB. > > Is there a recommended way to setup things? Like perhaps, e.g., having the mysql admin just create needed databases and giving all rights just to these DBs to galaxy like in: > > create database somedb; > grant all privileges on somedb.* to someusr@"localhost" identified by > 'passwrd'; > > and then have Galaxy work with that? But for that I'd need to know which DBs Galaxy uses and I have to set up. > > If not, I'll do the all privileges on *.*, but I don't really like that. > > Regards, > Bastien > > PS: sorry for nagging, but I'd really like to have a basic security level > PPS: if the above looks like straight from some manual, yes it is. I'm no > MySQL expert, but a good Google search brings most of what I need to > know. > > -- > DSM Nutritional Products AG > R&D Human Nutrition & Health > Bioinformatics - Bldg. 203 / 115 > P.O. Box 2676 > CH-4002 Basel / Switzerland > Tel. +41 61 815 8264 > > > DISCLAIMER : > This e-mail is for the intended recipient only > If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. > If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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galaxy-user May 2010