September 2011 - galaxy-dev - lists.galaxyproject.org

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 01 Sep '11

01 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 01 Sep '11

01 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 01 Sep '11

01 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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database migration error 79->80 (NameError: name 'BigInteger' is not defined)
by Edward Kirton 01 Sep '11

01 Sep '11

hi, we are getting the following error migrating from 79 to 80. curiously, my own galaxy didn't have this problem, but another developer here was getting this error. i moved him from sqlite to postgres but that didn't help. thanks for any assistance, ed Migrating 79 -> 80... galaxy.model.migrate.check INFO 2011-08-31 13:15:31,446 Traceback (most recent call last): File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", line 67, in create_or_verify_database migrate_to_current_version( engine, db_schema ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-jeff/lib/galaxy/model/migrate/check.py", line 125, in migrate_to_current_version schema.runchange( ver, change, changeset.step ) File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 184, in runchange File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 100, in run File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 112, in _func File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 108, in module File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/script/py.py", line 65, in verify_module File "/house/groupdirs/genetic_analysis/jfroula/Projects/Galaxy/galaxy-depot/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/util/importpath.py", line 12, in import_path File "lib/galaxy/model/migrate/versions/0080_quota_tables.py", line 29, in <module> Column( "bytes", BigInteger ), NameError: name 'BigInteger' is not defined

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