August 2013 - galaxy-dev - lists.galaxyproject.org

Server error one LefSe
by Gil Sharon 04 Aug '13

04 Aug '13

Hi All, When using the Huttenhower LEfSe on the main, online, Galaxy I got a Server Error, (Server Error,An error occurred. See the error logs for more information. (Turn debug on to display exception reports here)) when tried to Format data for LEfSe. Was able to successfully use it yesterday, but now it seems to be down. This happened using three different browsers and on multiple retries.. Any help is appreciated.. (is there a way of getting around that step? Other steps seem to be working fine). Gil

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How to get the data-view on local instance just like the Galaxy Main ?
by Nikhil Mallela 04 Aug '13

04 Aug '13

Hi, A few days ago, I have installed the stable release of of Galaxy local instance on my Workstation & I am running it behind Apache web server proxy . In regard to the data snapshots, I've observed that, it is much more organized on the Galaxy main rather than on my local instance. For example, Take a look at these pictures: On my local instance: [image: Inline image 1] On the Galaxy main: (also, this [image: Inline image 4] is missing on my local instance) [image: Inline image 2] Also, when I click the view [image: Inline image 3] on my local instance,the headers of the data is not corresponding to its respective columns. So, how can I fine tune these ? Thanks in advance! Nikhil. -- ------------------------------------------------------------ Nikhil Vinod Mallela, M.Sc. University of Muenster, Institute of Bioinformatics, Neil-Stensen Str. 12-14, 48149, Muenster,Germany. Tel.: +49 0251 83 50006 Fax: +49 0251 83 53005Email: mallela@uni-muenster.dehttp://complex-systems.uni-muenster.de/------------------------------------------------------------

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I wrote a small script to reload tool pages
by Ben Gift 02 Aug '13

02 Aug '13

Hi, I wanted to reload xml tool wrapper pages without using the browser. Going off of this page... http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-March/009126.html I wrote a little python script that takes the tool name (the thing at the top of the xml wrapper file) as a parameter and reloads it. Setup: Run this command *curl --cookie-jar galaxy_cookie.txt --data-ascii 'email=YOUR_EMAIL_NAME%40GMAIL.COM&webapp=galaxy&password=YOUR_PASSWORD&login_button=Login' YOUR_GALAXY_WEBPAGE/user/login <http://dev1.ab.wurnet.nl:8086/user/login>* and afterwards make sure the galaxy-cookie.txt file is in the same directory as the python script. Next, if your instance isn't on localhost:8080, update the python file and change the localhosts to your instance's address. Run the python script as ./reload_tool.py --name="your tool name" For instance I run ./reload_tool.py --name="BWA for Illumina" and it reloads it. Hopefully attachments work on the mailing list. But here's a mirror if not: http://pastebin.com/jHbbizQV

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Missing Tool Shed installation errors
by Peter Cock 02 Aug '13

02 Aug '13

Hi again, Currently under "Latest revision: installation errors' my clinod tool is listed on the Test Tool Shed, yet I don't see any errors displayed here: http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/deb6cb2db22b Any clues? Thanks, Peter

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Re: [galaxy-dev] [galaxy-iuc] [patch] enabling rst rendered readme file in TS
by Peter Cock 02 Aug '13

02 Aug '13

On Fri, Jul 12, 2013 at 3:35 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote: > Hello Björn, > > This one has been applied in changeset 10219:a7edac403b6c, and all of > your patches are now running on the test tool shed. > > Thanks very much, > > Greg Von Kuster Hi Greg & Björn, I think supporting reStructuredText is a good idea, but should not be done automatically, consider: http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040 This README file is named with the extension *.txt and does not render nicely if treated as *.rst, things like "System Message: ERROR" and "System Message: WARNING" are shown to the user. I suggest that the ToolShed only render like this if the README file is using the *.rst extension, but otherwise default to plain text (e.g. no extension or *.txt files). Thanks, Peter

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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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