July 2012 - galaxy-dev - lists.galaxyproject.org

Adding the tag in tool xml file
by sshashi 05 Jul '12

05 Jul '12

Hi, is it possible to add the tag in tool_xml_file ? how can i add new tag in tool_xml_file ? if anyone is working on this , guide me .... Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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conflicting migration files
by Langhorst, Brad 05 Jul '12

05 Jul '12

When I merged brad chapmans code into galaxy-central two 0099 migration files are created. I got things working by moving the ngs lims one to 0104 , but now i think i'll be in for a problem when a new 104 is created... What's the right way to solve this? Brad -- Brad Langhorst langhorst(a)neb.com<mailto:langhorst@neb.com> 978-380-7564

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Question about compressed files
by Ciara Ledero 05 Jul '12

05 Jul '12

Hi all, My colleague tried to upload via filesystem path a file with an approximate size of 2GB. It was a compressed file (filename.fq.gz). No error was reported, so I thought everything went fine, but when he tried running a tool, the uploaded file did not show in the input dropdown. But when he tried again, this time using an uncompressed file, every thing worked well. Now to my question: by default, can Galaxy accept and use compressed files? Or do I have to change something in its configuration just to do so? Thanks for the help! CL

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Byte-range support for IGV ?
by Chebbi Mohamed Amine 04 Jul '12

04 Jul '12

HELLO ! I just updated our local galaxy instance and just wanted to try the new IGV display application. When I try to display a BAM file whith the local IGV, I encounter the following message : "HTTP and FTP access to BAM files require byte-range support" Has anyone encountred the same probleme? Thanks in advances Regards Amine

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how to add new Xml tag in tool xml file
by sshashi 04 Jul '12

04 Jul '12

Hi, I am using my local instance of galaxy . I want to create a tag which will open an new window in galaxy. How can i create a new tag in tool_xml_file ? for this any modification is required in any file of galaxy ? Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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how to create a new tag in tool_xml_file of galaxy
by sshashi 04 Jul '12

04 Jul '12

Hi, I am using my local instance of galaxy . I want to create a tag which will open an new window in galaxy. How can i create a new tag in tool_xml_file ? for this any modification is required in any file of galaxy ? Regards shashi ------------------------------------------------------------------------------------------------------------------------------- This e-mail is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies and the original message. Any unauthorized review, use, disclosure, dissemination, forwarding, printing or copying of this email is strictly prohibited and appropriate legal action will be taken. -------------------------------------------------------------------------------------------------------------------------------

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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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