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Re: [galaxy-dev] Server Error after fresh installation of Galaxy
by Iry Witham 03 Jul '12

03 Jul '12

I am still experiencing issues getting my galaxy server to start since the upgrade. The logs are all getting this type of error: galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> cat runner0.log python path is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/boto-2.2.2-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/mercurial-2.1.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/docutils-0.7-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib, /usr/lib/python26.zip, /usr/lib64/python2.6, /usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk, /usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload, /usr/lib64/python2.6/site-packages/Numeric, /usr/lib64/python2.6/site-packages/gtk-2.0, /usr/local/lib64/python2.6/site-packages, /usr/lib64/python2.6/site-packages galaxy.model.migrate.check DEBUG 2012-07-03 12:35:03,580 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/app.py", line 35, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/galaxy/model/migrate/check.py", line 103, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '101' but this code expects version '97'. Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'. Removing PID file runner0.pid I have not dropped my database and built it fresh. However, I have attempted the recommended 'sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade' for both the runner and web app ini files with the following error: galaxy@galaxy2:/hpcdata/galaxy-test/galaxy-setup/galaxy-dist> sh manage_db.sh -c ./universe_wsgi.webapp.ini upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in <module> main( repository=repo, url=db_url ) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 327, in _migrate changeset = schema.changeset(version) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 173, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py", line 170, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py", line 145, in version return self.versions.version(*p, **k) File "/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py", line 125, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(101)> Any suggestions? Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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Display IGV link within history bam items?
by Chebbi Mohamed Amine 03 Jul '12

03 Jul '12

Hi ! I'am trying to set IGV as a display application in Galaxy. So I have addedin datatypes_conf.xml, under the bam datatype the display application for igv/bam (<display file="igv/bam.xml" />). However the Links dose not appear in bam history items. I see only " display in IGB Local<http://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826…> Web<http://genecloud.abgenomica.com/genecloud/display_application/07174ce6fe826…>" Could someone help me . Thanks Amine

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bug in transferring files in Galaxy to the UCSC browser
by David Gilmour 03 Jul '12

03 Jul '12

Hi, For some time now, we have found that wig files on the Penn State Galaxy cannot be transferred into the UCSC browser via the Galaxy URL. We receive the error: " Error Unrecognized format line 2 of https://main.g2.bx.psu.edu/datasets/329241/display/: (note: chrom names are case sensitive)". When we examine the file, the case is correct. Moreover, if we download the file and upload it to the UCSC browser directly from our computer, the data is properly displayed. A search of the Mailing List with the following phrase: "note: chrom names are case sensitive", brings up some discussion of this issue but I was unable to find a resolution. Thanks ********************************************* David S. Gilmour Professor of Biochemistry and Molecular Biology Center for Eukaryotic Gene Regulation Department of Biochemistry and Molecular Biology 465A North Frear Penn State University University Park, PA 16802 Office: 814-863-8905 Lab: 814-865-3795 Fax: 814-863-7024 Cellphone: 814-777-4166 Research web page: http://bmb.psu.edu/directory/dsg11 BMB Department: http://bmb.psu.edu/ Center for Eukaryotic Gene Regulation: http://www.huck.psu.edu/institutes-and-centers/cgr

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how to add check-boxes and button in new page
by Neetu Ojha 03 Jul '12

03 Jul '12

Hello, The first thing is absolutely new to the python. I am trying to integrate data-grid with GALAXY to host the pubchem data. For doing so I have created one .mako to add page and added one function in user.py. it adds one button as shown in the attachment. on click of the button it redirects to new page where the output is displayed as shown in the image file galaxy-op.png in attachment. My requirment is to have check boxes against the list of the files and add one button upload in the page shown in the file attached galaxy-op.png, which when clicked upload the data from the data-grid using some python script to local point. Kindly guide on that what to do. The changes done so far i present down: In the file /root/galaxy-dist/lib/galaxy/web/controllers/user.py Added : def gsrm_data( self, trans, webapp='galaxy'): # session = trans.sa_session # user = session.query( model.User ).filter_by( username=username ).first() user = trans.get_user() prxy="/root/x509up_u3163" refresh_frames = [ 'masthead'] os.environ["X509_USER_PROXY"]=prxy os.environ["PATH"]=os.environ["PATH"]+":/usr/local/GLOBUS-4.0.8/bin/:/usr/local/dpm/bin/:/usr/local/glite/bin" os.environ["LD_LIBRARY_PATH"]="/usr/local/GLOBUS-4.0.8/lib:/usr/local/dpm/lib:/usr/local/dpm/lib64:/usr/local/glite/lib" os.putenv('LD_LIBRARY_PATH', "/usr/local/GLOBUS-4.0.8/lib:/usr/local/dpm/lib:/usr/local/dpm/lib64:/usr/local/glite/lib") os.environ["DPM_HOST"]="gsrm" os.environ["DPNS_HOST"]="gsrm" proc = subprocess.Popen(['dpns-ls -l /dpm/ ctsf.cdac.org.in/home/OSDD/pubchem',prxy], shell=True, stdout=subprocess.PIPE,stdin=subprocess.PIPE) gsrm_output=proc.communicate()[0] sub_str=gsrm_output.split() index=8 count=0 str1='<table><tr><td>'+user.email+user.username+"slno"+'</td><td>'+"Gsrm_FileName "+'</td><td>'+"GSRM_URL"+'</td></tr><tr><td>' while (index < len(sub_str)): count=count+1 str1=str1+str(count)+'</td><td>'+sub_str[index]+'</td><td></td><td>'+"/dpm/ ctsf.cdac.org.in/home/OSDD/pubchem/"+sub_str[index]+'</td></tr><tr><td>' index = index + 9 str1=str1+'</td></tr></table>' return trans.fill_template( '/sindex.mako', webapp=webapp, refresh_frames=refresh_frames, message=str1, status='done', active_view="user" ) @web.expose created /root/galaxy-dist/templates/sindex.mako <%! def inherit(context): if context.get('webapp'): webapp = context.get('webapp') else: webapp = 'galaxy' return '/webapps/%s/base_panels.mako' % webapp %> <%inherit file="${inherit(context)}"/> <%namespace file="/messagex.mako" import="render_msg" /> <%def name="init()"> <% self.has_left_panel=False self.has_right_panel=False self.message_box_visible=False self.active_view="user" self.overlay_visible=False %> </%def> <%def name="stylesheets()"> ${parent.stylesheets()} <style> div#center { padding: 10px; } </style> </%def> <%def name="title()">Galaxy :: Logout</%def> <%def name="center_panel()"> ${self.body()} </%def> <%def name="body()"> %if message: ${render_msg( message, status )} %endif </%def> ___________________________________________________________________________________________ Please help!!!! Regards Neetu Sharma

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problems installing mothur via toolshed
by Hollander, Mattias de 03 Jul '12

03 Jul '12

Hi, I am trying to install the mothur toolsuite via the toolshed but this returns in an HTTP 500 error: URL: http://galaxy.nioo.knaw.nl/admin_toolshed/install_repository?tool_shed_url=… File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxyTools/galaxy-central/lib/galaxy/web/controllers/admin_toolshed.py', line 451 in install_repository clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) File '/home/galaxyTools/galaxy-central/lib/galaxy/util/shed_util.py', line 286 in clone_repository rev=[ ctx_rev ] ) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/commands.py', line 1157 in clone branch=opts.get('branch')) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/hg.py', line 350 in clone destrepo.clone(srcrepo, heads=revs, stream=stream) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/localrepo.py', line 2280 in clone return self.pull(remote, heads) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/localrepo.py', line 1582 in pull remotephases = remote.listkeys('phases') File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/wireproto.py', line 115 in plain encresref.set(self._submitone(f.func_name, encargsorres)) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/wireproto.py', line 163 in _submitone return self._call(op, **args) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/httprepo.py', line 169 in _call fp = self._callstream(cmd, **args) File '/home/galaxyTools/galaxy-central/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg/mercurial/httprepo.py', line 117 in _callstream resp = self.urlopener.open(req) File '/usr/lib/python2.7/urllib2.py', line 397 in open response = meth(req, response) File '/usr/lib/python2.7/urllib2.py', line 510 in http_response 'http', request, response, code, msg, hdrs) File '/usr/lib/python2.7/urllib2.py', line 435 in error return self._call_chain(*args) File '/usr/lib/python2.7/urllib2.py', line 369 in _call_chain result = func(*args) File '/usr/lib/python2.7/urllib2.py', line 518 in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error Any ideas how to fix this? Thanks!

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Trackster : samtools not found error
by Yec'han Laizet 03 Jul '12

03 Jul '12

Hello, I try to use the visualization tool of my local instance of galaxy under ubuntu. Everytime I try to create a feature track from a sam file, I get the following error: /bin/sh samtools not found I have installed samtools from ubuntu reposotories and it works well as I can call it from the shell. Nevertheless, I still get the same error. I checked that the samtools binary is in a folder included in my $PATH as described here: http://dev.list.galaxyproject.org/Re-bin-sh-samtools-not-found-gt-gt- WORKAROUND-td4585265.html I tried to use an "analyze data" tool in galaxy interface that uses samtools and it worked. It seems that it's only in trackster that samtools are not found. Do you have an idea to fix it? Best regards Yec'han ============================ Yec'han LAIZET Ingénieur Plateforme Genome Transcriptome Tel: 05 57 12 27 75 _________________________________ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ============================

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FastQC Tool Errors
by Josh Nielsen 02 Jul '12

02 Jul '12

Hello, I am having an issue with getting the FastQC tool to work with Galaxy on our server. I downloaded the FastQC files (version 0.8.0) and changed the directory that the wrapper script looks for the 'fastqc' executable in, but when we run a job with it we have been getting the following output: "Started analysis of Clip Approx 5% complete for Clip Approx 10% complete for Clip ... ... Approx 95% complete for Clip Approx 100% complete for Clip Analysis complete for Clip (.:9754): Gtk-WARNING **: cannot open display: " And then the job shows as failed in Galaxy. The output .dat file just has that same output/error message in it (though it seems to indicate it got to 100%). Also when I try to execute the fastqc file directly (albeit with no arguments) I get this: "Exception in thread "main" java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:173) at java.awt.Window.<init>(Window.java:437) at java.awt.Frame.<init>(Frame.java:419) at java.awt.Frame.<init>(Frame.java:384) at javax.swing.JFrame.<init>(JFrame.java:174) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:271) at uk.ac.bbsrc.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:102)" Both errors seem to have something to do with the graphical GUI component of FastQC (which I have seen some screenshots for on the FastQC webpage). If this application is GUI-driven how did the online PSU Galaxy get it to work with their wrapper script when the tools are run in a command-line environment with no X11 or Gtk? Essentially I'm just wondering what steps I'm missing here to getting this to work with our Galaxy mirror, other than just dropping the executable in place? Any suggestions? Thanks, Josh

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sanitizer for carriage return
by Jennifer Jackson 02 Jul '12

02 Jul '12

___________________________________________________________ On 7/1/12 3:05 AM, Katrien Bernaerts wrote: > Dear, > I am making a Galaxy appliciation with a text area. In the text area, > the user can copy/paste sequences. However, all carriage returns (e.g. > after the comment line) are converted to XX by Galaxy. I found that a > sanitizer can be used for specal characters, but I could not figure > out how to configure the sanitizer for a carriage return. Does anyone > have an idea how to handle carriage returns in the user input? > Thanks in advance, > -- > Katrien Bernaerts > > > The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org

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GMOD Summer School application deadline
by Scott Cain 02 Jul '12

02 Jul '12

Hello, The deadline to apply for the GMOD Summer School is in one week, July 9th. The application is available as a Google Form: https://docs.google.com/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LU… In the GMOD Summer School (August 24-29, 2012) we will cover the installation, configuration and use of a variety of GMOD tools, including Chado, GBrowse, JBrowse and Galaxy. For more information on the course, see the course web page at http://gmod.org/wiki/2012_GMOD_Summer_School The course will make heavy use of the Amazon Web Service (aka, the Cloud) via a grant from Amazon. Enrollment is limited to 24 students, and the application process is competitive: the last few years we've received over 75 applications for those 24 spots. I look forward to seeing you in North Carolina in August! -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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error running workflow
by J.W.F.van_der_Heijden＠lumc.nl 02 Jul '12

02 Jul '12

Hi all, I have added some tools to my local install of Galaxy. To get to my final results I have to do a lot of steps. When I try to run every step separately it turns out to work out fine. But when I try to run all steps at once with a workflow I get the following error message. OperationalError: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2012-07-02 11:34:48.135419', 'queued', 529] I have noticed that the processes eat a lot of my computer resources. Other than that I have no clue what the problem could be. Any tips are appreciated. Kind regards, Jaap van der Heijden

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