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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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import local files
by Ryan Golhar 30 Apr '10

30 Apr '10

Hi - I recently discovered Galaxy and am just getting started with it... I installed a local instance to test with NGS data. We have a lot of NGS datasets (both Solid and illumina) on a SAN available via NFS. Each user that has data has an account on the system in a directory tree such as: /ngsdata/user1 /ngsdata/user2 /ngsdata/project1 /ngsdata/project2 where user1 and user2 are distinct users with their own dataset, and project1, project2 contain datasets shared by multiple users. I want to import this data in Galaxy and I came across this thread in the mailing list (quoted below). I set up my Galaxy instance to see this NFS share...btw Galaxy is running as its own user on a virtual machine. The Galaxy user only has read access to this read and nothing else. When I went to import the files by specifying a local system path on the admin user interface, I got errors importing the data. I checked the paster.log file and I saw errors related to galaxy trying to change the permissions of the files to 0644. Does this mean all the files need to be owned by Galaxy? ------------------- Old thread: Hello Andreas, The best approach to handle this is to have a Galaxy administrator upload the files into a library, creating library datasets. Set the following config setting to point to the NFS accessible directory you use to contain the files: # Directories of files contained in the following directory can be uploaded to a library from the Admin view library_import_dir = /var/opt/galaxy/import You can set ACCESS permissions on the library to restrict access to specific users, or leave it public to allow anyone to access the library datasets. Users can import the library datasets into their own histories for analysis - doing this does not create another disk file, but simply a "pointer" to the library dataset's disk file. Greg Von Kuster Galaxy Development Team Andreas Kuntzagk wrote: > Hi, > > to reduce traffic when importing big dataset into our local galaxy we > would like to copy directly from the fileserver (which is accessible > from the galaxy server via NFS) into galaxy without moving through the > users desktop computer. > Is there already such a tool by chance? At a glance I could only find > import.py which imports only from a predefined set of files. > So if no such tool exist what would be the best starting point? > upload.py? > For security reasons I would restrict the import to a certain directory. > Anything else to keep in mind? > > regards, Andreas > _______________________________________________ > galaxy-user mailing list > galaxy-user at bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > >

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orthologus regions
by research pal 30 Apr '10

30 Apr '10

From: research pal <workinformatics(a)yahoo.com> Hi, I have a bed file for the chimp genome and I want to download the same region for the human genome. Do you have a tool in Galaxy which can help me for these orthologus regions. warm regards, Amit.

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universe_wsgi.ini -- "true" case sensitivity?
by Erick Antezana 30 Apr '10

30 Apr '10

Hi, some options in the file 'universe_wsgi.ini' are written 'true' (e.g. *use_new_layout = true*) and others 'True' (e.g. *static_enabled = True*). I was wondering whether using any of them is fine? cheers, Erick

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apache_xsendfile = true
by Erick Antezana 30 Apr '10

30 Apr '10

Hi, is there a way to test that the option apache_xsendfile = true is doing its job? (a log file message or so)? thanks, Erick

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Error uploading large files
by Linda Barnum 30 Apr '10

30 Apr '10

Hello, I am using a local install of galaxy for processing Illumina data. However, for large (about 3 GB) files, it gives an error and while it appears as if the upload is progressing, nothing happens. File "/home/lin/public_html/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py", line 818, in str_POST keep_blank_values=True) File "/usr/lib64/python2.6/cgi.py", line 508, in __init__ self.read_multi(environ, keep_blank_values, strict_parsing) File "/usr/lib64/python2.6/cgi.py", line 635, in read_multi headers = rfc822.Message(self.fp) File "/usr/lib64/python2.6/rfc822.py", line 108, in __init__ self.readheaders() File "/usr/lib64/python2.6/rfc822.py", line 155, in readheaders line = self.fp.readline() File "/usr/lib/python2.6/site-packages/paste/httpserver.py", line 476, in readline data = self.file.readline(max_read) File "/usr/lib64/python2.6/socket.py", line 379, in readline bline = buf.readline(size) OverflowError: signed integer is greater than maximum ---------------------------------------- 127.0.0.1 - - [13/Apr/2010:12:14:00 +0600] "GET /history HTTP/1.1" 200 - " http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (X11; U; Linux x86_64; en-US) AppleWebKit/533.2 (KHTML, like Gecko) Chrome/5.0.342.7 Safari/533.2" What could be going wrong? Thanks. Lin

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Re: [galaxy-user] [galaxy-bugs] cDNA mapping 454
by Jeremy Goecks 28 Apr '10

28 Apr '10

Hi Chris, I'm cc'ing galaxy-user because your questions are more about use than bugs. > Do you have any suggestiong for mapping cDNA reads using Lastz? > > I imagine the gaps caused by splicing cause problems for mapping cDNA reads using the commonly used setting? You're correct here. > Maybe setting up a "cDNA" mapping setting would be helpful, if such a thing is possible with LastZ. I looked through the LastZ documentation but didn't see anything that would support mapping cDNA to a reference genome. > > I suppose an alternative would be to map with bowtie, trimming all the reads to be equal length? You could try this, but splicing is likely to prevent good mapping. A better alternative is to use Tophat: http://tophat.cbcb.umd.edu/ Tophat is a splice junction mapper; Tophat, among other outputs, provides a list of mapped reads in SAM format. We have a very simple version of Tophat running on our test server that you try out: http://test.g2.bx.psu.edu/ We'll have a more complete version of Tophat up in the next day or two. A caveat: Tophat is designed for Illumina data, so you may not get optimal results when using 454 data. Best, J.

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Re: [galaxy-user] galaxy-user Digest, Vol 46, Issue 13
by Ross 27 Apr '10

27 Apr '10

Jelle, thanks for pointing out this dead-end link - now fixed - for the record, bitbucket marks any link preceded by 'wiki:' to be an unsafe URL... For the most up-to-date information on the WGA/SNP tools http://rgenetics.org is a good place to look. > Message: 6 > Date: Mon, 26 Apr 2010 09:03:14 +0200 > From: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> > To: galaxy <galaxy-user(a)bx.psu.edu> > Subject: [galaxy-user] rgenetics and atlas > Message-ID: > <u2wb66932c31004260003y3754116ev99cde23351ac6e6e(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I was wondering where I could find all the rgenetics dependencies as > the link at the bottom of: > http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies > doesn't seem to bring me anywhere. > Furthermore it seems that I'm missing the module atlas for genetrack, > although I haven't seen anything about the need for this dependency. > Should this be added as a dependency or is this an egg that should be > automatically fetched? > > Cheers, > Jelle

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how to create and use workflows
by Martin Senger 26 Apr '10

26 Apr '10

I am a new Galaxy user and I am trying to find out more about creation and usage of workflows. Once you have a workflow, its usage seems to be quite straighforward. But for the workflow creation, I am still looking for more documentation. I am especially interested in these topics: * How can I start a workflow with data from my computer if the upload step is not available for workflows? * What should I do for my new tools (added in my own Galaxy installation) to be able to participate in workflows. Anything specila to add in their XML description file perhaps? [Perhaps this question is more for the galaxy-dev mailing list?] * Is there perhaps more documentation on Galaxy workflows anywhere? Thanks for any help, Martin -- Martin Senger email: martin.senger@gmail.com,martin.senger@kaust.edu.sa skype: martinsenger

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