September 2009 - galaxy-user - lists.galaxyproject.org

after copy of galaxy not starting
by Andreas Kuntzagk 24 Sep '09

24 Sep '09

Hi, to run a second copy of local galaxy I just copied the whole directory (cp -ra <old_dir> <new_dir>) I then just edited the universe_wsgi.ini to use a different port. Now when I start run.sh in <new_dir> I get following error: galaxy.jobs INFO 2009-09-24 13:03:27,136 job stopper started Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> command.run() File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 78, in run File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 117, in invoke File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/command.py", line 212, in run File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 227, in command File "<new_dir>/eggs/py2.5-noplatform/PasteScript-1.3.6-py2.5.egg/paste/script/serve.py", line 250, in loadapp File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 193, in loadapp File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 214, in loadobj File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 606, in create File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/loadwsgi.py", line 99, in invoke File "<new_dir>/eggs/py2.5-noplatform/PasteDeploy-1.3.1-py2.5.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "<old_dir>/lib/galaxy/web/buildapp.py", line 68, in app_factory File "<old_dir>/lib/galaxy/web/buildapp.py", line 38, in add_controllers File "<new_dir>/lib/galaxy/web/controllers/page.py", line 9, in <module> class PageListGrid( grids.Grid ): NameError: name 'grids' is not defined As you may notice there are some files in the stacktrace from old_dir. Even more confusing is, that I renamed <old_dir> in the meantime. So these files are nonexistant. Where are these pathes hardcoded? regards, Andreas

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Bug: using the python builtin "id" as parameter or variable name
by Andreas Kuntzagk 21 Sep '09

21 Sep '09

Hi, we encountered this problem when trying to clone a shared workflow: ... File '/data/bioinformatics/galaxy/lib/galaxy/web/security/__init__.py', line 45 in decode_id return int( self.id_cipher.decrypt( id.decode( 'hex' ) ).lstrip( "!" ) ) AttributeError: 'builtin_function_or_method' object has no attribute 'decode' (full error message attached) So looks like the python builtin "id" is used in a few places - which causes problems. Don't know why nobody else encountered this. For reasons explained regarding the other bug I can't switch to a newer version then 2690 at the moment but from bitbucket it seems this is still there. regards, Andreas 141.80.188.104 - - [21/Sep/2009:16:44:47 +0200] "GET /history/list_shared HTTP/1.1" 200 - "http://141.80.186.51:8080/" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9" 141.80.188.104 - - [21/Sep/2009:16:45:01 +0200] "POST /history/list_shared?sort=-update_time HTTP/1.1" 500 - "http://141.80.186.51:8080/history/list_shared" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9" Error - <type 'exceptions.AttributeError'>: 'builtin_function_or_method' object has no attribute 'decode' URL: http://141.80.186.51:8080/history/list_shared?sort=-update_time File '/data/bioinformatics/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ File '/data/bioinformatics/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py', line 80 in __call__ File '/data/bioinformatics/galaxy/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ File '/data/bioinformatics/galaxy/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/framework/__init__.py', line 69 in decorator return func( self, trans, *args, **kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/controllers/history.py', line 280 in list_shared return self.clone( trans, id, **new_kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/framework/__init__.py', line 69 in decorator return func( self, trans, *args, **kwargs ) File '/data/bioinformatics/galaxy/lib/galaxy/web/controllers/history.py', line 751 in clone history = get_history( trans, history_id, check_ownership=False ) File '/data/bioinformatics/galaxy/lib/galaxy/web/controllers/history.py', line 781 in get_history id = trans.security.decode_id( id ) File '/data/bioinformatics/galaxy/lib/galaxy/web/security/__init__.py', line 45 in decode_id return int( self.id_cipher.decrypt( id.decode( 'hex' ) ).lstrip( "!" ) ) AttributeError: 'builtin_function_or_method' object has no attribute 'decode' CGI Variables ------------- CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded' HTTP_ACCEPT: 'application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-us' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=eb142648ac45b770fb93d51daf5785c6dd869b6b4503e8d7958db670bf3f993b3c3866342008fd05' HTTP_HOST: '141.80.186.51:8080' HTTP_ORIGIN: 'http://141.80.186.51:8080' HTTP_REFERER: 'http://141.80.186.51:8080/history/list_shared' HTTP_USER_AGENT: 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_5_8; en-us) AppleWebKit/531.9 (KHTML, like Gecko) Version/4.0.3 Safari/531.9' PATH_INFO: '/history/list_shared' QUERY_STRING: 'sort=-update_time' REMOTE_ADDR: '141.80.188.104' REQUEST_METHOD: 'POST' SERVER_NAME: '141.80.186.51' SERVER_PORT: '8080' SERVER_PROTOCOL: 'HTTP/1.1' Configuration ------------- __file__: '/data/bioinformatics/galaxy/universe_wsgi.ini' admin_users: 'dominic.tolle@mdc-berlin.de,matthias.dodt@mdc-berlin.de' brand: '"It\'s full of stars!"' bugs_email: 'mailto:dominic.tolle@mdc-berlin.de' database_file: 'database/universe.sqlite' datatype_converters_config_file: 'datatype_converters_conf.xml' datatype_converters_path: '/data/bioinformatics/galaxy/lib/galaxy/datatypes/converters' datatype_indexers_path: '/data/bioinformatics/galaxy/lib/galaxy/datatypes/indexers' debug: 'False' default_cluster_job_runner: 'sge:///' error_email_to: 'dominic.tolle(a)mdc-berlin.de' file_path: 'database/files' gbrowse_display_sites: 'main,test' here: '/data/bioinformatics/galaxy' id_secret: 'changethisinproductiontoo' job_queue_cleanup_interval: '30' job_scheduler_policy: 'galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin' log_events: 'True' log_level: 'DEBUG' log_memory_usage: 'False' mailing_join_addr: 'galaxy-user-join(a)bx.psu.edu' new_file_path: 'database/tmp' sendmail_path: '/usr/sbin/sendmail' session_data_dir: '/data/bioinformatics/galaxy/database/beaker_sessions' session_key: 'galaxysessions' session_secret: 'changethisinproduction' session_type: 'file' set_metadata_externally: 'False' start_job_runners: 'sge' static_cache_time: '360' static_dir: '/data/bioinformatics/galaxy/static/' static_enabled: 'True' static_favicon_dir: '/data/bioinformatics/galaxy/static/favicon.ico' static_images_dir: '/data/bioinformatics/galaxy/static/images' static_scripts_dir: '/data/bioinformatics/galaxy/static/scripts/' static_style_dir: '/data/bioinformatics/galaxy/static/june_2007_style/blue' tool_config_file: 'tool_conf.xml' tool_data_path: 'tool-data' tool_path: 'tools' ucsc_display_sites: 'main,test,archaea' use_beaker_session: 'True' use_interactive: 'False' use_lint: 'False' use_new_layout: 'true' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x2efafd0> paste.cookies: (<SimpleCookie: galaxysession='eb142648ac45b770fb93d51daf5785c6dd869b6b4503e8d7958db670bf3f993b3c3866342008fd05'>, 'galaxysession=eb142648ac45b770fb93d51daf5785c6dd869b6b4503e8d7958db670bf3f993b3c3866342008fd05') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x2e57d90> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0xcde250> paste.parsed_querystring: ([('sort', '-update_time')], 'sort=-update_time') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True webob._parsed_post_vars: (MultiDict([('id', '15a3f866c4811e6a'), ('operation', 'Clone')]), <FakeCGIBody at 332de90 viewing MultiDict([('id...e')])>) webob._parsed_query_vars: (MultiDict([('sort', '-update_time')]), 'sort=-update_time') wsgi process: 'Multithreaded' ------------------------------------------------------------

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import local files
by Andreas Kuntzagk 18 Sep '09

18 Sep '09

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

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History "disappearing" when using tags
by Andreas Kuntzagk 17 Sep '09

17 Sep '09

Hi, we just noticed a bug: we added a tag to history. Then we run a tool. After that the list of datasets in the right pane just disappeared. This is in rev 2690. Could not find any related update. regards, Andreas

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Re: [galaxy-user] [galaxy-bugs] a query
by Anton Nekrutenko 16 Sep '09

16 Sep '09

Gerome: This question is more applicable to our galaxy-user list, so I am redirecting it there. See the reply below. What you are trying to do is, in fact, quite easy to perform with galaxy: 1. Extend gene coordinates either direction with "Operate of Genomic Intervals->Get Flanks" 2. Join the newly extended genes with SNP dataset using "Operate of Genomic Intervals->Join" 3. Group by gene name and concatenate on SNP name using "Join, Subtract and Group -> Join". Please, see this history: http://main.g2.bx.psu.edu/history/imp?id=354aae8cd0d5e1c5 for an example. If you click on "rerun" link within history item (see attached image), you will be able to see parameters I've used. NOTE: There are two kind of join in Galaxy: relational join ("Join, Subtract and Group->Join") and interval join ("Operate of Genomic Intervals->Join"). Here we use interval join. If have any trouble I will make a galactic quickie (short movie) for you. Thanks, anton galaxy team On Sep 16, 2009, at 8:57 AM, Gerome Breen wrote: > Hi, > I am puzzled about how to generate something - can you help? I want to > generate a file with hapmap or other sets of snps mapped to UCSC > genes. I want to have one line per gene with the min start -20kb and > max end +20kb and then a tab sperated list of hapmap SNPs in each > gene. I have tried to do this but failed - the one line per gene is > complicate by the fact that aggregate on column seems to discard the > chr information and a join within two coordinates doesn't seem to be > available but anyway would be very computationally intensive. Any > solutions would be appreciated. > > The file format I am aiming at: > > chr start end gene_name snp1 snp2 snp3 etc. > > Best > > Gerome. > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-bugs Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

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python 2.6
by Andreas Kuntzagk 16 Sep '09

16 Sep '09

Hi, I know that 2.6 is not supported right now (and we had some problems when we tried the latest version with 2.6) So are there any plans to move to 2.6 in the near future? regards, Andreas

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conditional statement
by Matthias Dodt 15 Sep '09

15 Sep '09

i would like to nest different conditional statements in a tools xml file: <inputs> <conditional name="tophat_input"> <param name="type1" type="select" label="input file format" optional="false"> <option value="fasta" selected="true">FASTA</option> <option value="fastqsolexa">FASTQ-Solexa</option> <option value="fastqsanger">FASTQ-Sanger</option> </param> <when value="fasta"> <conditional name="paired_end_fasta"> <param name="type2" type="select" label="Paired end reads"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> .... how do i access type2? #if $tophat_input.paired_end_fasta.type2=="yes": #--value=test #end if doesnt work! thanks mat

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Workflows not saving
by Daniel Klevebring 15 Sep '09

15 Sep '09

Dear list, I have a problem saving workflows, every time I click the save button, the dialog saying "Saving..." comes up but never disappears. I can't click on anything, bu have to reload the page. When I then check the workflow, nothing is saved. This happenes to me using Firefox3@Fedora10, Firefox3.5(a)MacOsX10.5 and Safari(a)MacOsX10.5, both on the public Galaxy and on our local copy. Has anyone else seen this? Thanks Daniel

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various import dir's
by Erick Antezana 15 Sep '09

15 Sep '09

Hi, how can I defined various library import directories within the "universe_wsgi.ini" by using the "library_import_dir" ? same question for "user_library_import_dir"? thanks, Erick

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Update galaxy
by Andreas Kuntzagk 15 Sep '09

15 Sep '09

Hi, I tried to update our local galaxy installation. I'm quite unexperienced with Mercurial so I read up something on the web how to update. What I did is: hg pull hg update After that I tried to restart but got an error message that I need to run "sh manage_db.sh upgrade" which I did. So now it is running again. But when I connect I see in the main screen: "Galaxy build: $Rev" which is an old version. Does that mean something in my update failed? (I did not get any messages that hinted at some problems beside the database version.) Or was just some template not updated? regards, Andreas

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