- galaxy-dev - lists.galaxyproject.org

Adding an OpenID provider to Galaxy
by Nikolai Vazov 06 Sep '11

06 Sep '11

Hi, I have been trying to add a new OpenID provider to the Galaxy-hardcoded list of providers. I type in my credentials in the new provider's window, but I got the following error (I am giving here only the last five lines) .... Module openid.consumer.consumer:413 in complete Module openid.message:167 in fromPostArgs Module openid.message:200 in _fromOpenIDArgs Module openid.message:240 in setOpenIDNamespace InvalidOpenIDNamespace: Invalid OpenID Namespace u'http%3A%2F%2Fspecs.openid.net%2Fauth%2F2.0' Does anybody have an idea what in my server goes wrong with the OpenID Namspace and how I can fix it? It might be useful to say that my Galaxy database is located on a separate machine with an SSL connection form the Galaxy app server. Thank you in advance Nikolai -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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Problems with load_workflow_editor
by shashi shekhar 03 Sep '11

03 Sep '11

Hi All, i am not able to create workflow in my local instance of galaxy. it's displaying only loading picture on browser when i am clicking on edit option of workflow . how can we resolve such type of problem ? i am using old version version galaxy. 192.168.60.115, 145.139.1.156 - - [02/Sep/2011:16:13:50 +0600] "GET /workflow/get_datatypes?_=1314940546255 HTTP/1.1" 200 - " http://garu.ac.in/workflow/editor?id=df7a1f0c02a5b08e" "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.17) Gecko/20110420 Firefox/3.6.17" 192.168.60.115, 145.139.1.156 - - [02/Sep/2011:16:13:51 +0600] "GET /workflow/load_workflow?_=1314940546462&id=df7a1f0c02a5b08e&_=true HTTP/1.1" 200 - "http://garu.ac.in/workflow/editor?id=df7a1f0c02a5b08e" "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.2.17) Gecko/20110420 Firefox/3.6.17" Regards shashi shekhar

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deleting files from galaxy database/file system
by Nikhil Joshi 03 Sep '11

03 Sep '11

Hi all, How does galaxy handle deletion of files? I mean when I delete a file from my history, it doesn't seem like it deletes it from the database directory, nor does it delete any associated "files" directories. Is it scheduled for deletion and will be deleted at some point? Is there any way to force the deletion, besides simply deleting the files directly on our server? If I did that, would that be a problem? Any help would be highly appreciated! Thanks! - Nik.

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Re: [galaxy-dev] Modifying OpenID providers
by Nate Coraor 03 Sep '11

03 Sep '11

Hi Nikolai, It's best to send questions directly to the mailing list, so they reach the widest audience and the right people. There are some responses below: Nikolai Vazov wrote: > > Hi, Nate, > > You helped me install Galaxy with a DB hosted on a remote server via > SSL connection. Thanks a lot again for your help. > > I have been struggling to add OpenID providers to Galaxy, but have > not been very successful. I have some questions: > > 1) Where are the variables (OpenID providers) in the dropdown menu > stocked? In a file, the DB? The template (login.mako) has a line > > > <%def name="render_openid_form( referer, auto_associate, > openid_providers )"> > > but the where are the date for openid_providers (I am a newby in > python ...) > > 2) In which files do you configure them? The list is hardcoded in: lib/galaxy/web/controllers/user.py These should ultimately be moved to a configuration file. > 3) The provider I want to add uses SAML 2.0, which is the package I > need for python? pysaml2.0? I haven't worked with SAML before so unfortunately I can't be of much help here. --nate > > Thank you for your help > > Nikolai > > -- > Nikolay Vazov, PhD > Research Computing Centre - http://hpc.uio.no > USIT, University of Oslo

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Problem with workflow
by shashi shekhar 02 Sep '11

02 Sep '11

Hi, i am not able to create workflow in my local instance of galaxy. it's displaying only loading picture on browser. i am using old version version galaxy. Regards shashi shekhar

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problem in workflow
by shashi shekhar 02 Sep '11

02 Sep '11

Hi All, I am using local instance of galaxy,i am not able to use workflow .when i am clicking on workflow , it' displaying the loading picture only . i am not able to see workflow editor. may it depends on browser........? Regards shashi

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contribute tools to galaxy?
by Dongjun Chung 02 Sep '11

02 Sep '11

Hi All, I'm a newbie to galaxy and enjoying it a lot these days. Thanks for the great work. I have a question regarding contribution of software to galaxy. We developed a ChIP-seq peak calling algorithm and software (R package) and hope to contribute it to galaxy. I have read the wiki and prior mailing list about the contribution system but it is still somewhat confusing to me. 1. It seems that I can contribute our software to "tool shed" if I prepare appropriate code & definition files. Then, users can download and use it with their locally installed galaxy. However, these files committed to tool shed will not appear in galaxy main or test servers. Am I correct? 2. What is clear relationship between main/test servers & tool shed? Can we contribute our software to main or test servers as well? Or only galaxy core developers can add new tools to galaxy main or test servers? If so, which software is considered to be added to servers? Are they chosen from tools contributed to tool shed? 3. If our software is a R package, then users need to download and install it first in their R system before they use our software within their galaxy system even in the case they have appropriate definition files. Am I right? Or is there any better solution for this? Thanks! Best, Dongjun

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accessing files_path directory in subsequent analysis steps
by Nikhil Joshi 02 Sep '11

02 Sep '11

Hi all, So I am writing XML files for an analysis pipeline. The first step in the pipeline is to index the reference, the resulting files of which I have put into the files_path directory that I get from using $output.files_path. But then I want to be able to get access to that path in a subsequent step when I choose the output of the indexing step as the input to the next step. So I have the user choose the indexed output (which is just an html page with links to the indexed reference files), and then I try to use $input.files_path.... and that doesn't work. Am I thinking about this in the right way? How would I find the files_path that was created for the output of the previous step so that I can use it as an input directory for the current step? - Nik

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VCF 4.1 support
by Lance Parsons 02 Sep '11

02 Sep '11

Galaxy is currently using vcfPytools for vcf support in a few tools as well as for viewing in Trackster. Unfortunately, vcfPytools does not support the latest version of vcf (4.1) and thus is causing issues when used with the output of many newer variant callers such as Freebayes. I contacted the author of vcfPytools about this and he had this to say: I have actually completely rewritten the tool in C++ (now imaginatively called vcfCTools!). This supports v4.1, but is not quite complete and requires some additional testing. This should not take too long (perhaps another week), but then I will make this new version available on github and you are more than welcome to use this. I can let you know when I push the code. The rewrite is designed with freeBayes in mind and is being tested with vcf outputs from its most recent version. If there are specific problems/concerns that you have, please let me know and I'll make sure that I address these. Al Is anyone working on modifying Galaxy to use the new vcfCTools? I would be willing to lend my support to such an effort. If not, is there at least support from the Galaxy team for doing this? -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Re: [galaxy-dev] Display BAM with IGV
by Iry Witham 01 Sep '11

01 Sep '11

Hi Everyone, I have been tasked with getting the IGV working within our Galaxy instance. I have modified our Nginx configuration based on the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. The IGV viewer component in Galaxy does not display the results from a BAM file in either the web or local instance of IGV. I have tested with IGV1.5 and with version 2.03. Neither produce a visual representation of the sequence. When attempting to use the web option we get the same error provided in the original post as noted below. Has anyone gotten this to work with Nginx-0.8.53 or any of the newer versions? Thanks, Iry Witham Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org On Apr 27, 2011; 10:06am “Hello all, I just updated our local copy of Galaxy and just wanted to try the new IGV display application. When I try to display a BAM file with the local IGV or the web IGV I encounter following error complaining about the Null content-length. Has any of you encountered the same problem? Do I miss something? Thanks in advance Alex INFO [2011-04-27 16:00:14,440] [TrackManager.java:225] [Thread-6] Loading1 resources. ERROR [2011-04-27 16:00:14,589] [SeekableHTTPStream.java:59] [Thread-6] Null content-length for: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… ERROR [2011-04-27 16:00:14,590] [TrackLoader.java:821] [Thread-6] Error loading sam track java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… NULL content-length at org.broad.igv.util.SeekableHTTPStream.<init>(SeekableHTTPStream.java:60) at org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42) at org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129) at org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70) at org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80) at org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97) at org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75) at org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:69) at org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54) at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761) at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143) at org.broad.igv.track.TrackManager.load(TrackManager.java:271) at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241) at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282) at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148) at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88) at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193) at org.broad.igv.main.CommandListener.run(CommandListener.java:93) at java.lang.Thread.run(Thread.java:636) ERROR [2011-04-27 16:00:14,592] [TrackLoader.java:211] [Thread-6] java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/45… NULL content-length” On Apr 27, 2011; 12:33pm “Hi Alex, Displaying BAM files at external applications usually requires an http server that supports partial gets. Unfortunately, the current lightweight http server that is built into Galaxy does not support these advanced http options. However, this limitation can be overcome by using a proxy server that is able to handle http1.1 requests. Please see "Using a Proxy server" at https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for help on setting this up. Thanks for using Galaxy, Dan” On Apr 27, 2011; 9:07pm “I’m getting this same error and I’m running nginx as a proxy server. Is there a specfic parameter we should be aware of to allow partial gets? I don’t see anything in the wiki page for setting up the ProductionServer. Thanks, Dave” On May 04, 2011; 7:47am “Could someone who has successfully gotten the IGV tool to work using NGINX as your proxy, tell me if there was anything specific they needed to do with their NGINX or galaxy config to get it working? Thanks, Dave” On May 09, 2011; 2:52pm “It's necessary to set up the more advanced configuration under "Sending files using nginx" on the nginxProxy page in the wiki. Could you let us know whether you're using that configuration or just a basic pass-through proxy? Thanks, --nate”

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