- galaxy-dev - lists.galaxyproject.org

account marked
by Kumar, Charu Gupta 02 Aug '13

02 Aug '13

Hi, I tried to login into my account today (cgkumar1(a)gmail.com<mailto:cgkumar1@gmail.com>) and found that it has been marked for deletion. I have been doing some active analysis in that account, and the results have not been downloaded yet. When I had been notified about the account, I had indicated that it should be kept active. But looks like there was some confusion. I look forward to seeing the account and analysis restored. Thank you so much. Best wishes, Charu Gupta Kumar, Ph.D.

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Printing the current date in a param value
by Frédéric Sapet 02 Aug '13

02 Aug '13

Hello Is there a way to do something like this ? <param name="dateAnalyse" format="txt" type="text" size="25" value="${time.strftime('%Y_%m_%d')}" label="Date de l'analyse" help="15/01/2012" optional="True"/> I would like to set a kind of default value to my param. ${time.strftime('%Y_%m_%d')} is not interpreted. I have tried this because it works within the label attribute in <data> tag (for labeling my output) But it does not work for the label attribute (neither value attribute) in <param> tab. thank you. Fred

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Choosing which nodes to run on for a whole history (Galaxy cluster)
by Ben Gift 02 Aug '13

02 Aug '13

I'm setting up Galaxy and Torque with my cluster and I was wondering if I could set it up so that nodes could be assigned for a whole history. This way I can re-run histories on certain nodes for benchmarking runtimes. It seems that the closest I can get with the built in functionality is specifying nodes on a per-tool basis, which is good but it would be painful to have to specify this for each tool I use in a pipeline each time. So how difficult would it be for me to add this feature, and which files should I start with in the code base? Or have I misunderstood and this is actually built in? Thanks

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Toolshed repository update error
by S.D. Hiltemann 02 Aug '13

02 Aug '13

I am working on putting a tool into the toolshed. I have a bash script wrapper. I uploaded the first version fine, but when I wanted to upload a revision, some unwanted characters are inserted around the revised function of my code (see bottom) ..the inserted "<<<<<< local" etc strings are causing my script to fail of course. How can I prevent this from happening? Saskia snippet of the code: if [[ ! -s $rfile ]] then dummycol=${addcols:2} outputcol=${dummycol//",B."/" "} <<<<<<< local echo -e "${col_chr_name}\t${col_start_name}\t${col_end_name}\t${col_ref_name}\t${col_obs_name}\t$outputcol" > $rfile cat $rfile ======= numcommas=`echo "$addcols" | grep -o "," | wc -l` echo "numcolums: $numcommas" awk 'BEGIN{FS="\t";OFS="\t"}{ if(FNR==1) print $0,"'"$outputcol"'"; else{ printf $0 for(i=0;i<="'"$numcommas"'"+1;i++) printf "\t" printf "\n" } }END{}' $ofile > tempofile mv tempofile $ofile return >>>>>>> other fi

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Sudden error in local galaxy installation
by Raj Ayyampalayam 02 Aug '13

02 Aug '13

Hello, My local cluster based galaxy installation was running fine till this evening. Later I decided to test some workflows and got an error with massive stack trace. I can't make any sense of this. Here is the last part of the error. The stack trace is literally 1000's of lines. Can somebody throw some light on this? Thanks, -Raj File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/datatypes/data.py", line 483, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/__init__.py", line 2264, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 201, in execute db_dataset = trans.db_dataset_for( input_dbkey ) File "/panfs/pstor.storage/home/qbcglab/galaxy_run/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 1046, in db_dataset_for for ds in datasets: File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py", line 2227, in __iter__ return self._execute_and_instances(context) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py", line 2242, in _execute_and_instances result = conn.execute(querycontext.statement, self._params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1576, in _execute_clauseelement inline=len(distilled_params) > 1) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py", line 1778, in compile return self._compiler(dialect, bind=bind, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py", line 1784, in _compiler return dialect.statement_compiler(dialect, self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 276, in __init__ engine.Compiled.__init__(self, dialect, statement, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 705, in __init__ self.string = self.process(self.statement) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 724, in process return obj._compiler_dispatch(self, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 997, in visit_select t = select._whereclause._compiler_dispatch(self, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 498, in visit_clauselist for c in clauselist.clauses) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 496, in <genexpr> s for s in File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 498, in <genexpr> for c in clauselist.clauses) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 618, in visit_binary **kw File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 663, in _operator_dispatch return fn(OPERATORS[operator]) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 617, in <lambda> self, **kw), File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/visitors.py", line 72, in _compiler_dispatch return getter(visitor)(self, **kw) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 679, in visit_bindparam name = self._truncate_bindparam(bindparam) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 743, in _truncate_bindparam bind_name = self._truncated_identifier("bindparam", bind_name) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/compiler.py", line 754, in _truncated_identifier anonname = name.apply_map(self.anon_map) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/expression.py", line 1325, in apply_map return self % map_ RuntimeError: maximum recursion depth exceeded -- Bio-informatics consultant QBCG (http://qbcg.uga.edu) 706-542-6092 (8-12 All week) 706-583-0442 (12-5 All week)

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Velvet optimizer: Running two long paired files.
by Perez, Ricardo 01 Aug '13

01 Aug '13

Dear all, Today when running velvet oprimizer vlsci, we encountered that if you use two long files as input then the output is a file that its description is "no peek". However when I run the files seperately the velvet optimizer seems to work fine. I am not sure if this is a bug or not. Thank you for your time, --Ricardo Perez

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Error message
by Mark Edward Fabreag 01 Aug '13

01 Aug '13

Good day! While I was uploading the file (through FileZilla), I encountered this message box: [image: Inline image 1] Will this affect uploading process? Thank you.

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extract metadata
by Christian Dreischer 01 Aug '13

01 Aug '13

Hi there, I'm looking for an elegant way to extract the metadata for a Galaxy history item from a PostgreSQL database. My special interest lies in the path to the output file and the input parameters. Has by any chance anybody already done this and a ready to use python script at hand? ;) Thanks, Chris

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enable to edit pages
by Philipe Moncuquet 01 Aug '13

01 Aug '13

Hi guys, Since the last update of Galaxy. We are enable to edit pages on our local instance. Pages can be viewed without problems but not editing. The server error we get is as foolow, any advice would be greatly appreciated. URL: http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33… Module galaxy.web.framework.middleware.error:*149* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.recursive:*84* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*190* in handle_request >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> body *=* method*(* trans*,* ****kwargs *)* Module galaxy.web.framework:*98* in decorator >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* func*(* self*,* trans*,* ***args*,* ****kwargs *)* Module galaxy.webapps.galaxy.controllers.page:*446* in edit_content >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* trans*.*fill_template*(* "page/editor.mako"*,* page*=*page *)* Module galaxy.web.framework:*957* in fill_template >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* self*.*fill_template_mako*(* filename*,* ****kwargs *)* Module galaxy.web.framework:*969* in fill_template_mako >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* template*.*render*(* ****data *)* Module mako.template:*296* in render >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* runtime*.*_render*(*self*,* self*.*callable_*,* args*,* data*)* Module mako.runtime:*660* in _render >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> ****_kwargs_for_callable*(*callable_*,* data*)**)* Module mako.runtime:*692* in _render_context >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> _exec_template*(*inherit*,* lclcontext*,* args*=*args*,* kwargs*=*kwargs*)* Module mako.runtime:*718* in _exec_template >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> callable_*(*context*,* ***args*,* ****kwargs*)* Module _base_base_panels_mako:*125* in render_body >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> __M_writer*(*unicode*(*self*.*center_panel*(**)**)**)* Module page_editor_mako:*196* in render_center_panel >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> __M_writer*(*unicode*(*page*.*latest_revision*.*content*.*decode*(*'utf-8'*) **)**)* Module encodings.utf_8:*16* in decode >> <http://galaxy-dev.bioinformatics.csiro.au/page/edit_content?id=f2db41e1fa33…> *return* codecs*.*utf_8_decode*(*input*,* errors*,* True*)* *UnicodeEncodeError: 'ascii' codec can't encode character u'\u2019' in position 1709: ordinal not in range(128)* * * Regards, Philippe

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Next Galaxy Release date (and Tool Shed update)?
by Peter Cock 01 Aug '13

01 Aug '13

Hi all, Is there a target date for the next Galaxy release, or should that differ, the next update to the main Tool Shed? I'd like to start using reStructuredText README.rst files in my tools which render much more nicely on the Test Tool Shed, but are currently ignored on the Main Tool Shed (since it doesn't yet have the updates to look for and display *.rst files). Thanks, Peter

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