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[hg] galaxy 3413: lims: added feature to to transfer folders fro...
by Greg Von Kuster 19 Feb '10

19 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/bbff5050cfd2 changeset: 3413:bbff5050cfd2 user: rc date: Thu Feb 18 11:50:19 2010 -0500 description: lims: added feature to to transfer folders from a sequencer diffstat: lib/galaxy/web/controllers/requests_admin.py | 63 ++++++++++++++------------- 1 files changed, 32 insertions(+), 31 deletions(-) diffs (94 lines): diff -r e05cdf1205bc -r bbff5050cfd2 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Feb 18 11:26:39 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Feb 18 11:50:19 2010 -0500 @@ -1146,7 +1146,7 @@ for index in range(len(sample.request.samples)): # check for empty bar code if not barcode.strip(): - msg = 'Please fill the barcode for sample <b>%s</b>.' % samples[index].name + msg = 'Please fill the barcode for sample <b>%s</b>.' % sample.name break # check all the saved bar codes all_samples = trans.sa_session.query( trans.app.model.Sample ) @@ -1401,9 +1401,19 @@ sample_id=trans.security.encode_id(sample.id), msg=msg, messagetype='error', folder_path=folder_path )) - files = output.split()[2:] - return files - + return output.split()[2:] + + def __get_files_in_dir(self, trans, sample, folder_path): + tmpfiles = self.__get_files(trans, sample, folder_path) + for tf in tmpfiles: + if tf[-1] == os.sep: + self.__get_files_in_dir(trans, sample, os.path.join(folder_path, tf)) + else: + sample.dataset_files.append([os.path.join(folder_path, tf), + sample.transfer_status.NOT_STARTED]) + trans.sa_session.add( sample ) + trans.sa_session.flush() + return @web.expose @web.require_admin def get_data(self, trans, **kwd): @@ -1460,19 +1470,24 @@ sample=sample, dataset_files=sample.dataset_files) elif params.get( 'start_transfer_button', False ): - for f in files_list: - if f[-1] == os.sep: - # the selected item is a folder so transfer all the - # folder contents - sample.dataset_files.append([os.path.join(folder_path, f), - sample.transfer_status.NOT_STARTED]) - else: - sample.dataset_files.append([os.path.join(folder_path, f), - sample.transfer_status.NOT_STARTED]) - trans.sa_session.add( sample ) - trans.sa_session.flush() - return self.__start_datatx(trans, sample) - + folder_files = [] + if len(files_list): + for f in files_list: + if f[-1] == os.sep: + # the selected item is a folder so transfer all the + # folder contents + self.__get_files_in_dir(trans, sample, os.path.join(folder_path, f)) + else: + sample.dataset_files.append([os.path.join(folder_path, f), + sample.transfer_status.NOT_STARTED]) + trans.sa_session.add( sample ) + trans.sa_session.flush() + return self.__start_datatx(trans, sample) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_datatx_page', + sample_id=trans.security.encode_id(sample.id), + folder_path=folder_path)) + def __setup_datatx_user(self, trans, library, folder): ''' This method sets up the datatx user: @@ -1562,20 +1577,6 @@ dataset_index=index, cmd=cmd) dtt.start() -# # set the transfer status -# sample.dataset_files[index][1] = sample.transfer_status.IN_PROGRESS -# trans.sa_session.add( sample ) -# trans.sa_session.flush() -# try: -# retcode = subprocess.call(cmd) -# except Exception, e: -# error_msg = dfile.split('/')[-1] + ": Data transfer failed. " + str(e) + "<br/>" -# return trans.response.send_redirect( web.url_for( controller='requests_admin', -# action='show_datatx_page', -# sample_id=trans.security.encode_id(sample.id), -# folder_path=os.path.dirname(dfile), -# messagetype='error', -# msg=error_msg)) # set the sample state to the last state if sample.current_state().id != sample.request.type.states[-1].id: event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1],

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[hg] galaxy 3412: Added mm5 to the list of manual builds
by Greg Von Kuster 19 Feb '10

19 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e05cdf1205bc changeset: 3412:e05cdf1205bc user: gua110 date: Thu Feb 18 11:26:39 2010 -0500 description: Added mm5 to the list of manual builds diffstat: tool-data/shared/ucsc/manual_builds.txt | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (9 lines): diff -r 0c07212afc00 -r e05cdf1205bc tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Thu Feb 18 09:47:21 2010 -0500 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu Feb 18 11:26:39 2010 -0500 @@ -668,3 +668,4 @@ arabidopsis Arabidopsis thaliana TAIR9 arabidopsis_tair8 Arabidopsis thaliana TAIR8 araTha1 Arabidopsis thaliana TAIR7 +mm5 Mouse May 2004 (mm5) \ No newline at end of file

1 0

Fwd: QueuePool error
by SHAUN WEBB 18 Feb '10

18 Feb '10

Hi Galaxy Team, I sent this query last week and was wondering if anyone new anything about this error. I closed and re-started Galaxy to get it going again, however I have had to do this twice this week whenever we have multiple people using the server (3) and one is running a large workflow (15 steps). Also, we are having an additional problem when trying to convert large tabular files to interval. The file is over 12 million lines, we are getting a server time out error as I assume Galaxy tries to inspect the entire file before changing format. Thanks Shaun Webb Hi, our Galaxy server is showing a timeout error: TimeoutError: QueuePool limit of size 10 overflow 20 reached, connection timed out, timeout 30 I assume this is due to overuse as it is consistent with the database settings in the universe.wsgi file. First of all, is there anyway to view and cancel queued jobs? I usually use the admin page but this is not accessible at the moment. Secondly, we plan for Galaxy to be used on a large scale, is there anyway of preventing this type of error in future? I've included the full traceback below. Thanks in advance for any help Shaun Webb URL: http://bifx3.bio.ed.ac.uk:8080/admin Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred >> environ, self.app) Module paste.wsgilib:539 in intercept_output << data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ << environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(>> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ << []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)>> return self.application(environ, start_response) Module galaxy.web.framework.base:99 in __call__ << rc.environ = environ # Setup the transaction trans = self.transaction_factory( environ ) rc.redirect = trans.response.send_redirect # Get the controller class >> trans = self.transaction_factory( environ ) Module galaxy.web.framework:110 in <lambda> << def __init__( self, galaxy_app, session_cookie='galaxysession' ): base.WebApplication.__init__( self ) self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) # Mako support self.mako_template_lookup = mako.lookup.TemplateLookup(>> self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) Module galaxy.web.framework:150 in __init__ << self.workflow_building_mode = False # Always have a valid galaxy session self.__ensure_valid_session( session_cookie ) # Prevent deleted users from accessing Galaxy if self.app.config.use_remote_user and self.galaxy_session.user.deleted:>> self.__ensure_valid_session( session_cookie ) Module galaxy.web.framework:279 in __ensure_valid_session << galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, self.app.model.GalaxySession.table.c.is_valid==True ) ) \ .first() # If remote user is in use it can invalidate the session, so we need to to check some things now. >> self.app.model.GalaxySession.table.c.is_valid==True ) ) Module sqlalchemy.orm.query:1300 in first << ret = list(self)[0:1] else: ret = list(self[0:1]) if len(ret) > 0: return ret[0]>> ret = list(self[0:1]) Module sqlalchemy.orm.query:1221 in __getitem__ << return list(res)[None:None:item.step] else: return list(res) else: return list(self[item:item+1])[0]>> return list(res) Module sqlalchemy.orm.query:1361 in __iter__ << if self._autoflush and not self._populate_existing: self.session._autoflush() return self._execute_and_instances(context) def _execute_and_instances(self, querycontext):>> return self._execute_and_instances(context) Module sqlalchemy.orm.query:1364 in _execute_and_instances << def _execute_and_instances(self, querycontext): result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) return self.instances(result, querycontext)>> result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) Module sqlalchemy.orm.session:754 in execute << engine = self.get_bind(mapper, clause=clause, **kw) return self.__connection(engine, close_with_result=True).execute( clause, params or {})>> return self.__connection(engine, close_with_result=True).execute( Module sqlalchemy.orm.session:721 in __connection << return self.transaction._connection_for_bind(engine) else: return engine.contextual_connect(**kwargs) def execute(self, clause, params=None, mapper=None, **kw):>> return engine.contextual_connect(**kwargs) Module sqlalchemy.engine.base:1229 in contextual_connect << """ return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) def table_names(self, schema=None, connection=None):>> return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) Module sqlalchemy.pool:142 in connect << def connect(self): if not self._use_threadlocal: return _ConnectionFairy(self).checkout() try:>> return _ConnectionFairy(self).checkout() Module sqlalchemy.pool:304 in __init__ << self.__counter = 0 try: rec = self._connection_record = pool.get() conn = self.connection = self._connection_record.get_connection() self._connection_record.backref = weakref.ref(self, lambda ref:_finalize_fairy(conn, rec, pool, ref))>> rec = self._connection_record = pool.get() Module sqlalchemy.pool:161 in get << def get(self): return self.do_get() def do_get(self):>> return self.do_get() Module sqlalchemy.pool:628 in do_get << return self.do_get() else: raise exc.TimeoutError("QueuePool limit of size %d overflow %d reached, connection timed out, timeout %d" % (self.size(), self.overflow(), self._timeout)) if self._overflow_lock is not None:>> raise exc.TimeoutError("QueuePool limit of size %d overflow %d reached, connection timed out, timeout %d" % (self.size(), self.overflow(), self._timeout)) TimeoutError: QueuePool limit of size 10 overflow 20 reached, connection timed out, timeout 30 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev ----- End forwarded message ----- -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

Issue with boolean parameters in Galaxy
by Tam, Oliver 18 Feb '10

18 Feb '10

Hi, I have recently noticed a strange behavior with boolean parameters. The XML files are treating all boolean values as true when sending instructions to tools. This means that regardless of whether the boolean box is checked, the value of the parameter is always true. Tools with boolean parameters works fine with changeset 3372:4a6bb3b64012 But fails with changeset 3373:a3e6350ffc57 I have attached an XML that I¹ve been using to test this behavior (boolean_value_test.xml), which outputs yes (for a true value) and no (for a false value). Cheers, Oliver

2 1

[hg] galaxy 3411: Fix CheckboxField.is_checked(), which was brok...
by Greg Von Kuster 18 Feb '10

18 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0c07212afc00 changeset: 3411:0c07212afc00 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Feb 18 09:47:21 2010 -0500 description: Fix CheckboxField.is_checked(), which was broken if change set 3373. diffstat: lib/galaxy/web/form_builder.py | 2 -- templates/library/common/select_template.mako | 9 ++++++--- 2 files changed, 6 insertions(+), 5 deletions(-) diffs (39 lines): diff -r 4a416d872806 -r 0c07212afc00 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Wed Feb 17 16:37:02 2010 -0500 +++ b/lib/galaxy/web/form_builder.py Thu Feb 18 09:47:21 2010 -0500 @@ -102,8 +102,6 @@ def is_checked( value ): if value == True: return True - if isinstance( value, basestring ) and value.lower() in ( "yes", "true", "on" ): - return True # This may look strange upon initial inspection, but see the comments in the get_html() method # above for clarification. Basically, if value is not True, then it will always be a list with # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not diff -r 4a416d872806 -r 0c07212afc00 templates/library/common/select_template.mako --- a/templates/library/common/select_template.mako Wed Feb 17 16:37:02 2010 -0500 +++ b/templates/library/common/select_template.mako Thu Feb 18 09:47:21 2010 -0500 @@ -1,6 +1,10 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<% + from galaxy.web.form_builder import CheckboxField + inheritable_check_box = CheckboxField( 'inheritable' ) +%> <script type="text/javascript"> $( function() { $( "select[refresh_on_change='true']").change( function() { @@ -50,10 +54,9 @@ <div class="form-row"> <label>Inherit template to contained folders and datasets?</label> %if inheritable_checked: - <input type="checkbox" name="inheritable" value="yes" checked/>Yes - %else: - <input type="checkbox" name="inheritable" value="yes"/>Yes + <% inheritable_check_box.checked = True %> %endif + ${inheritable_check_box.get_html()} <div class="toolParamHelp" style="clear: both;"> Check if you want this template to be used by other folders and datasets contained within this ${item_desc} </div>

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Re: [galaxy-dev] [galaxy-bugs] Fwd: Fwd: Installing data for Galaxy
by Daniel Blankenberg 18 Feb '10

18 Feb '10

Hi Iwe, > In the datatypes_conf.xml I added: > <datatype extension="fastabench" type="galaxy.sequence:Fasta" display_in_upload="true"/> All FASTA type files (fasta, fastabench, etc.) will be valid input for the 'fastabench' datatype. If you want to have a unique datatype that only includes 'fastabench' datatypes, you will need to create a new datatype class; if you want this datatype to be valid for 'fasta' input as well, this datatype should subclass Fasta. For example, in lib/galaxy/datatypes/sequence.py, add: class FastaBench( Fasta ): """Class representing a FASTA bench sequence""" file_ext = "fastabench" and change the entry in datatypes_conf.xml to (assuming you want it visible in the upload display): <datatype extension="fastabench" type="galaxy.sequence:FastaBench" display_in_upload="true"/> Also, confirm by looking at the screen output when starting the galaxy server via run.sh that the datatype is loading properly, if a datatype cannot be loaded properly it will default back to text. > Also when I choose an already existing (present in datatypes_conf.xml) format like "codcmp", and I add: > <param format="codcmp" name="input5" type="data" label="codcmp list example"/> > the list shows all the files in the file history tab. Correct, the codcmp datatype is of class galaxy.datatypes.data:Text, so all text files are valid codcmp files. Let us know how it goes and if we can be of further assistance. Thanks, Dan On Feb 18, 2010, at 7:09 AM, Iwe Muiser wrote: > Hey Dan, > > In the datatypes_conf.xml I added: > <datatype extension="fastabench" type="galaxy.sequence:Fasta" display_in_upload="true"/> > > Then in the XML file of the tool I added: > <param format="fastabench" name="input2" type="data" label="fastabench list example"/> > > Also when I choose an already existing (present in datatypes_conf.xml) format like "codcmp", and I add: > <param format="codcmp" name="input5" type="data" label="codcmp list example"/> > the list shows all the files in the file history tab. It seems to only work well with the very standard formats like fasta, BED, wig and so on. But I can not find the proper place to add my new datatype so that it will be shown in a list. > > Iwe > > > > 2010/2/17 Daniel Blankenberg <dan(a)bx.psu.edu> > Hi Iwe, > > Can you provide copies of the relevant sections of your datatypes_conf.xml, the actual datatype you created as well as the tool's xml file? > > Thanks, > > Dan > > On Feb 17, 2010, at 8:23 AM, Daniel Blankenberg wrote: > >> >> >> Begin forwarded message: >> >>> From: Iwe Muiser <e.c.muiser(a)gmail.com> >>> Date: February 17, 2010 6:14:24 AM EST >>> To: Daniel Blankenberg <dan(a)bx.psu.edu> >>> Subject: Re: [galaxy-bugs] Fwd: [galaxy-dev] Installing data for Galaxy >>> >>> Hello Dan, >>> >>> I tried and it's not working. I also deleted the underscores which also doesn't seem to help. A form keeps showing all the files in my history instead of the files with the new datatype I set. I have the idea I did not set the datatype correctly in a certain file, but I can't find which one it should be. >>> >>> Iwe >>> >>> 2010/2/16 Daniel Blankenberg <dan(a)bx.psu.edu> >>> Hello Iwe, >>> >>> Have you tried using all lowercase characters for the extension of your new datatype, including in the datatypes_conf.xml file? >>> >>> Thanks, >>> >>> Dan >>> >>> >>> >>> On Feb 16, 2010, at 10:55 AM, Guruprasad Ananda wrote: >>> >>>> Hi Iwe, >>>> >>>> I'm forwarding your message to galaxy-bugs mailing list so that the right person can help you. >>>> >>>> Thanks, >>>> Guru. >>>> >>>> Begin forwarded message: >>>> >>>>> ---------- Forwarded message ---------- >>>>> From: Iwe Muiser <e.c.muiser(a)gmail.com> >>>>> Date: 2010/2/11 >>>>> Subject: Re: [galaxy-dev] Installing data for Galaxy >>>>> To: Guruprasad Ananda <gua110(a)bx.psu.edu> >>>>> >>>>> >>>>> Hello Guru, >>>>> >>>>> I have another question concerning adding a data format. I added a more stringent version of fasta to the datatypes as instructed on the website (adding to data_types.xml, building a sniffer, adding this to registry.py). Also I added a PWM datatype. I also installed a tool that needs PWM data as input (I set "format="PFMsimple""). If I upload a PWM file it will be automatically recognized as such. >>>>> However, when I want to make a file selection list for the tool that only shows the PWM files I run into problems. Instead of only showing the PWM format files, it shows all files present in the history. It does seem to work with fasta (or all regular file formats for that matter). I clearly forgot to set something right. Do you have a clue as to where to start? >>>>> >>>>> Thanks! >>>>> >>>>> Iwe >>>>> >>>>> >>>>> >>>>> On Feb 5, 2010, at 4:49 AM, Iwe Muiser wrote: >>>>> >>>>> > Hey Guru, >>>>> > >>>>> > Nate does not seem to answer. Is he absent or did something go wrong >>>>> > with the CC-ing? >>>>> > >>>>> > Greetings, >>>>> > >>>>> > Iwe >>>>> > >>>>> > 2010/2/3 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >> Hey Iwe, >>>>> >> >>>>> >> I'm glad you got it running! Please don't hesitate to email us if you have any questions in the future. >>>>> >> >>>>> >> Thanks for using Galaxy, >>>>> >> Guru. >>>>> >> >>>>> >> On Feb 3, 2010, at 4:59 AM, Iwe Muiser wrote: >>>>> >> >>>>> >>> Hey Guru, >>>>> >>> >>>>> >>> Thanks for the good description and cc-ing my other issue. I have >>>>> >>> installed several organisms now and it seems to be working perfectly. >>>>> >>> >>>>> >>> Greetings, >>>>> >>> >>>>> >>> Iwe >>>>> >>> >>>>> >>> 2010/2/2 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >>>> Hi Iwe, >>>>> >>>> >>>>> >>>> Yes, the path in alignseq.loc should contain the filename as well. For instance, here's how my alignseq.loc entry looks: >>>>> >>>> seq hg18 /Users/guru/Desktop/hg18.2bit.2bit >>>>> >>>> In fact, I tried downloading the 2bit file from UCSC just now, and updated my alignseq.loc and ran galaxy. The 'Extract genomic DNA' tool worked just fine and returned sequences. The only reason I could think why it isn't working for you is the alignseq.loc entry issue. Also, for some reason, the UCSC file has ".2bit" repeated twice in it's name. I'm sure you might have noticed that already. If not, please make sure the file name is ok. >>>>> >>>> >>>>> >>>> Also, I'm forwarding your email to Nate (on cc), who is the best person to help you with the issues you are facing with executing your binary. >>>>> >>>> >>>>> >>>> Please let us know if you have any further questions, >>>>> >>>> Guru. >>>>> >>>> >>>>> >>>> >>>>> >>>> On Feb 2, 2010, at 5:51 AM, Iwe Muiser wrote: >>>>> >>>> >>>>> >>>>> Hey Guru, >>>>> >>>>> >>>>> >>>>> There are some things I don't understand. I added the directory >>>>> >>>>> containing my binary executable to the PATH. if I open a terminal, it >>>>> >>>>> is able to find it by simply typing "32cotrasif_gw". When I make >>>>> >>>>> Galaxy execute the binary I get the following error: "An error >>>>> >>>>> occurred running this job: /bin/sh: 32cotrasif_gw: not found". it >>>>> >>>>> seems Galaxy uses sh to execute which does not seem to look at .bashrc >>>>> >>>>> or PATH variables. >>>>> >>>>> So I tried to set the interpreter to "bash". This gives the following >>>>> >>>>> error: "/home/muiser/Programs/galaxy_dist/tools/_motif_disc/32cotrasif_gw: >>>>> >>>>> /home/muiser/Programs/galaxy_dist/tools/_motif_disc/32cotrasif_gw: >>>>> >>>>> cannot execute binary file". >>>>> >>>>> >>>>> >>>>> "bash -c" needs quotes everywhere and makes the whole process >>>>> >>>>> unnecessarily complicated from my point of view (and has it never >>>>> >>>>> worked as well). >>>>> >>>>> >>>>> >>>>> A python wrapper script around cotrasif does make the output file >>>>> >>>>> (dataset_X.dat) but still gives me a red results item because it >>>>> >>>>> interprets the scripts standard output as faulty somehow. >>>>> >>>>> >>>>> >>>>> Do you have any ideas that might help me out? >>>>> >>>>> >>>>> >>>>> Also, the path to my hg18.2bit is set correctly. Mustn't I set the >>>>> >>>>> filename in this path as well? or just the path to the file itself? >>>>> >>>>> >>>>> >>>>> Greetings, >>>>> >>>>> >>>>> >>>>> Iwe >>>>> >>>>> >>>>> >>>>> 2010/2/1 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >>>>>> Hi Iwe, >>>>> >>>>>> >>>>> >>>>>> No, you don't need fasta files. Just the 2bit file should do. On looking at the python code for the tool, it seems like your PATH_TO_hg18.2bit may not be set correctly. Please make sure the path is right (and absolute) and try running the tool again. >>>>> >>>>>> >>>>> >>>>>> About your tool integration issue- please try using this format in the xml file, and let me know if it works fine: >>>>> >>>>>> <command> >>>>> >>>>>> myBinary $input $output >>>>> >>>>>> </command> >>>>> >>>>>> Also, please make sure that the binary is in your PATH. >>>>> >>>>>> >>>>> >>>>>> Thanks, >>>>> >>>>>> Guru. >>>>> >>>>>> >>>>> >>>>>> On Feb 1, 2010, at 1:17 PM, Iwe Muiser wrote: >>>>> >>>>>> >>>>> >>>>>>> Hello Guru, >>>>> >>>>>>> >>>>> >>>>>>> Thanks for the tip. It kind of works (no more red errors) except that >>>>> >>>>>>> it still doesn't actually fetches the sequences. >>>>> >>>>>>> The error is: >>>>> >>>>>>> "empty, format: fasta, database: hg18 >>>>> >>>>>>> Info: 55 warnings, 1st is: Chromosome by name 'chr1' was not found for >>>>> >>>>>>> build 'hg18'. >>>>> >>>>>>> Skipped 55 invalid lines, 1st is #1, "chr1 1259997 1260525 MACS_peak_6 0 +"" >>>>> >>>>>>> >>>>> >>>>>>> Do I also need the actual fasta files stored somewhere? I have them >>>>> >>>>>>> but I don't know where to put them so that galaxy can find them. >>>>> >>>>>>> >>>>> >>>>>>> Another problem I have is with integrating tools. I have a binary >>>>> >>>>>>> executable that gives a lot of trouble. I have tried everything from >>>>> >>>>>>> making a wrapper python script to all kinds of combinations with "./" >>>>> >>>>>>> and bash -c. Also I have put quotes pretty much everywhere. Now, >>>>> >>>>>>> finally, I have it working with a wrapper script only Galaxy gives me >>>>> >>>>>>> a message that the scripts stdout and sterror are actual errors while >>>>> >>>>>>> the file is being generated perfectly (dataset_X.dat). Do you know >>>>> >>>>>>> what is going on? >>>>> >>>>>>> I hope I made it clear enough because it is a nasty problem to explain. >>>>> >>>>>>> >>>>> >>>>>>> Iwe >>>>> >>>>>>> >>>>> >>>>>>> 2010/2/1 Guruprasad Ananda <gua110(a)bx.psu.edu>: >>>>> >>>>>>>> Hello Iwe, >>>>> >>>>>>>> I apologise for not covering data integration in detail on our wiki. >>>>> >>>>>>>> Here's how you add a new sequence to your Galaxy instance. In your case, for >>>>> >>>>>>>> hg18, please download hg18.2bit file >>>>> >>>>>>>> from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/, and then >>>>> >>>>>>>> update tool-data/alignseq.loc file with the following line: >>>>> >>>>>>>> seq hg18 PATH_TO_hg18.2bit >>>>> >>>>>>>> Also, in future if you want to find out which ".loc" file to use, you can >>>>> >>>>>>>> check the validator tag under the input parameter in the tool's xml file. >>>>> >>>>>>>> Please let us know if you need any more information. >>>>> >>>>>>>> Thanks, >>>>> >>>>>>>> Guru >>>>> >>>>>>>> Galaxy team. >>>>> >>>>>>>> >>>>> >>>>>>>> On Feb 1, 2010, at 9:39 AM, Iwe Muiser wrote: >>>>> >>>>>>>> >>>>> >>>>>>>> Hello, >>>>> >>>>>>>> >>>>> >>>>>>>> I have some questions about installing data onto my Ubuntu linux box. Mainly >>>>> >>>>>>>> genomic data that can be used by the extract_genomic_dna.py script. I have >>>>> >>>>>>>> done some attempts to get this working but now I'm quite stuck. First I >>>>> >>>>>>>> downloaded this data from the UCSC ftp site. >>>>> >>>>>>>> (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/chromosomes to be precise). >>>>> >>>>>>>> Then I added the following line to "faseq.loc" as instructed: "hg18 >>>>> >>>>>>>> /home/muiser/data/Human_data/HG18/chromosomes". >>>>> >>>>>>>> After this I restarted the galaxy deamon but nothing seems to have happened. >>>>> >>>>>>>> I have the idea that I am missing certain steps. >>>>> >>>>>>>> >>>>> >>>>>>>> The ultimate goal is to get a local galaxy install working like the one on >>>>> >>>>>>>> "http://main.g2.bx.psu.edu/" >>>>> >>>>>>>> >>>>> >>>>>>>> The wiki is helpful to install new tools and to get an idea of how stuff >>>>> >>>>>>>> works but sparsely mentions data integration. Except for MAFs which I tried >>>>> >>>>>>>> as well. I'm now building an index for these .maf files which I assume will >>>>> >>>>>>>> take quite some time. >>>>> >>>>>>>> >>>>> >>>>>>>> I hope you can help me out a bit. >>>>> >>>>>>>> >>>>> >>>>>>>> Thanks in advance, >>>>> >>>>>>>> >>>>> >>>>>>>> Iwe Muiser >>>>> >>>>>>>> _______________________________________________ >>>>> >>>>>>>> galaxy-dev mailing list >>>>> >>>>>>>> galaxy-dev(a)lists.bx.psu.edu >>>>> >>>>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>>>> >>>>>>>> >>>>> >>>>>>>> Guruprasad Ananda >>>>> >>>>>>>> Graduate Student >>>>> >>>>>>>> Bioinformatics and Genomics >>>>> >>>>>>>> The Pennsylvania State University >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> >>>>> >>>>>>> -- >>>>> >>>>>>> Master student >>>>> >>>>>>> Bioinformatics & Gene Regulation Group >>>>> >>>>>>> NTNU Trondheim >>>>> >>>>>>> +4594157082 >>>>> >>>>>>> >>>>> >>>>>> >>>>> >>>>>> Guruprasad Ananda >>>>> >>>>>> Graduate Student >>>>> >>>>>> Bioinformatics and Genomics >>>>> >>>>>> The Pennsylvania State University >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> Iwe EC Muiser >>>>> >>>>> Master student >>>>> >>>>> Bioinformatics & Gene Regulation Group >>>>> >>>>> NTNU Trondheim >>>>> >>>>> +4594157082 >>>>> >>>>> >>>>> >>>> >>>>> >>>> Guruprasad Ananda >>>>> >>>> Graduate Student >>>>> >>>> Bioinformatics and Genomics >>>>> >>>> The Pennsylvania State University >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> Iwe EC Muiser >>>>> >>> Master student >>>>> >>> Bioinformatics & Gene Regulation Group >>>>> >>> NTNU Trondheim >>>>> >>> +4594157082 >>>>> >>> >>>>> >> >>>>> >> Guruprasad Ananda >>>>> >> Graduate Student >>>>> >> Bioinformatics and Genomics >>>>> >> The Pennsylvania State University >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> >> >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > Iwe EC Muiser >>>>> > Master student >>>>> > Bioinformatics & Gene Regulation Group >>>>> > NTNU Trondheim >>>>> > +4594157082 >>>>> > >>>>> >>>>> Guruprasad Ananda >>>>> Graduate Student >>>>> Bioinformatics and Genomics >>>>> The Pennsylvania State University >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Iwe EC Muiser >>>>> Master student >>>>> NTNU - Department of Cancer Research and Molecular Medicine >>>>> Bioinformatics & Gene Regulation Group >>>>> Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 >>>>> Trondheim >>>>> +4594157082 >>>>> >>>>> >>>>> >>>>> -- >>>>> Iwe EC Muiser >>>>> Master student >>>>> NTNU - Department of Cancer Research and Molecular Medicine >>>>> Bioinformatics & Gene Regulation Group >>>>> Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 >>>>> Trondheim >>>>> +4594157082 >>>> >>>> >>>> Guruprasad Ananda >>>> Graduate Student >>>> Bioinformatics and Genomics >>>> The Pennsylvania State University >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> galaxy-bugs mailing list >>>> galaxy-bugs(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-bugs >>> >>> >>> >>> >>> -- >>> Iwe EC Muiser >>> Master student >>> NTNU - Department of Cancer Research and Molecular Medicine >>> Bioinformatics & Gene Regulation Group >>> Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 >>> Trondheim >>> +4594157082 >> >> _______________________________________________ >> galaxy-bugs mailing list >> galaxy-bugs(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-bugs > > > > > -- > Iwe EC Muiser > Master student > NTNU - Department of Cancer Research and Molecular Medicine > Bioinformatics & Gene Regulation Group > Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1 > Trondheim > +4594157082

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delete a galaxy user
by Emeric Dubois 18 Feb '10

18 Feb '10

Hello, I have installed Galaxy in a production environment for multiple users. My installation of Galaxy has been configured such that only users who are logged in may use it and only admin may create a new user. I have a problem, I can create but can't delete a account... For the moment, I use a mysql command to block account : UPDATE galaxy.galaxy_user SET deleted = 1 WHERE galaxy_user.email LIKE "emeric.dubois(a)gmail.com" ; By this command, the account is inactive but all data associated are in database and in dataset folder. To free disk space, a set of scripts exist to remove the data files (histories and deleted datasets) but I haven't found a script to delete a user and all his data in database and dataset folder. Can you tell me if you have a solution to cleanly delete a user and his data ? Thank you. Best regards Emeric -- ***************************************** Emeric Dubois Plateforme MGX Institut de Génomique Fonctionnelle UMR 5203 CNRS – U 661 INSERM – Universite de Montpellier 141 rue de la cardonille 34094 Montpellier Cedex 05, France Tel: 04 67 14 29 32 Emeric.Dubois(a)igf.cnrs.fr ***************************************** -- Ce message a été vérifié par MailScanner pour des virus ou des polluriels et rien de suspect n'a été trouvé.

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[hg] galaxy 3410: Fix bug introduced in change set 3408:6471c9b8...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4a416d872806 changeset: 3410:4a416d872806 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 16:37:02 2010 -0500 description: Fix bug introduced in change set 3408:6471c9b8149c when testing form fields with labels / values longer than 30 chars. diffstat: test/base/twilltestcase.py | 16 +++++++++------- 1 files changed, 9 insertions(+), 7 deletions(-) diffs (26 lines): diff -r a8b176655f0b -r 4a416d872806 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Feb 17 15:50:38 2010 -0500 +++ b/test/base/twilltestcase.py Wed Feb 17 16:37:02 2010 -0500 @@ -882,13 +882,15 @@ control.get( name=elem ).selected = True else: # control.is_of_kind( "singlelist" ) for elem in control_value: - # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py - if len( elem ) > 30: - elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) - else: - elem_name = elem - - tc.fv( f.name, control.name, str( elem_name ) ) + try: + tc.fv( f.name, control.name, str( elem ) ) + except Exception, e2: + # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py + if len( elem ) > 30: + elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + elem_name = elem + tc.fv( f.name, control.name, str( elem_name ) ) except Exception, exc: errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) errmsg += "control: %s\n" % str( control )

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[hg] galaxy 3409: Fix for bug introduced in change set 3386:8d9c...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a8b176655f0b changeset: 3409:a8b176655f0b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 15:50:38 2010 -0500 description: Fix for bug introduced in change set 3386:8d9c8cf65dee when downloading datasets from a library. diffstat: lib/galaxy/web/controllers/library_common.py | 3 +-- 1 files changed, 1 insertions(+), 2 deletions(-) diffs (13 lines): diff -r 6471c9b8149c -r a8b176655f0b lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Feb 17 14:49:13 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Feb 17 15:50:38 2010 -0500 @@ -1274,8 +1274,7 @@ or ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: continue ext = ldda.extension - if ext in composite_extensions: - is_composite = True + is_composite = ext in composite_extensions path = "" parent_folder = ldda.library_dataset.folder while parent_folder is not None:

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[hg] galaxy 3408: Fix bug intorduced in change set 3404:1e85451c...
by Greg Von Kuster 17 Feb '10

17 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6471c9b8149c changeset: 3408:6471c9b8149c user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Feb 17 14:49:13 2010 -0500 description: Fix bug intorduced in change set 3404:1e85451c9c86 if testing multiple check boxes. Functional tests will now correctly test uploaded file names longer than 30 characters. diffstat: test/base/twilltestcase.py | 17 ++++++++++++----- 1 files changed, 12 insertions(+), 5 deletions(-) diffs (32 lines): diff -r 68dac4d2d94a -r 6471c9b8149c test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Feb 17 13:54:44 2010 -0500 +++ b/test/base/twilltestcase.py Wed Feb 17 14:49:13 2010 -0500 @@ -872,16 +872,23 @@ try: checkbox = control.get() checkbox.selected = is_checked( control_value ) - except ClientForm.AmbiguityError: - # if there's more than one checkbox, use the behaviour for - # ClientForm.ListControl - see twill code.. - pass + except Exception, e1: + # if there's more than one checkbox, probably should use the behaviour for + # ClientForm.ListControl ( see twill code ), but this works for now... + for elem in control_value: + control.get( name=elem ).selected = True else: for elem in control_value: control.get( name=elem ).selected = True else: # control.is_of_kind( "singlelist" ) for elem in control_value: - tc.fv( f.name, control.name, str( elem ) ) + # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py + if len( elem ) > 30: + elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) + else: + elem_name = elem + + tc.fv( f.name, control.name, str( elem_name ) ) except Exception, exc: errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) ) errmsg += "control: %s\n" % str( control )

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