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

Re: [galaxy-dev] Toolshed tribulations--certain types seem unsupported
by Michael Moore 09 Apr '12

09 Apr '12

No joy. I cannot even find acknowledgement that galaxy is loading any of my tools or of those in the directory that follows. The tool is called analyze_reads and "cat paster.log| grep analyze_r| less produces an end of file. The last tool load showing is vcf_tools_extract, but all beyond that also load and are usable in workflows EXCEPT analyze_reads when any parameter is specified type="float" or type="integer". The tools I am using to edit the files are set for UTF-8 encoding but are not in fact capable of sending anything but plain old ASCII. (the very basic vi as my X isn't working at the moment). Still examining paster.log was an education. I am pleased that it got by many reported errors and still picked up my scan_reads tool. I guess my next act is to run siege and see if all the instances are actually responding Thank you much for the suggestion. I really needed to see paster.log. On Mon, Apr 9, 2012 at 3:28 PM, Ross <ross.lazarus(a)gmail.com> wrote: > Michael, > > First thing I'd do would be to check paster.log after trying to load > your new tool and I'll bet there's an 8 bit character or something in > your text somewhere that causes the tool parser to barf - the error in > paster.log will tell you the line and character where loading stopped? > > On Mon, Apr 9, 2012 at 6:24 PM, Michael Moore > <michaelglennmoore(a)gmail.com> wrote: > > I am testing galaxy for wide use, and I have legacy text files that call > > algorithms, sorts, and displays. One such has a tool.xml file with 10 > > parameters, one select, three integer, and one float, with the rest text > for > > the moment. (some will be type="data" later if the runs equate to the > runs > > we do outside galaxy) > > > > The tool does not show up. Firefox, emacs and vim all agree that it is > > well-formed, and galaxy has been properly bounced. I experimented with > > removing parameters and found with 7 parameters, I did not have the > problem, > > then I noticed that all of them had been changed to text or select in my > > desperation to make it show up for placement on the workflow. I > returned to > > 10 parameters, but this time all type="select" and type="text", and > > everything worked. But slipping even one integer, even with the > (optional) > > min max and default tags, and the tool would disappear on restart. > > > > Am I looking at a bug, or is there something I need to be doing to make > this > > tool visible with numeric parameters? > > > > MGM > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > -- > Ross Lazarus MBBS MPH; > Associate Professor, Harvard Medical School; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; >

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Toolshed tribulations--certain types seem unsupported
by Michael Moore 09 Apr '12

09 Apr '12

I am testing galaxy for wide use, and I have legacy text files that call algorithms, sorts, and displays. One such has a tool.xml file with 10 parameters, one select, three integer, and one float, with the rest text for the moment. (some will be type="data" later if the runs equate to the runs we do outside galaxy) The tool does not show up. Firefox, emacs and vim all agree that it is well-formed, and galaxy has been properly bounced. I experimented with removing parameters and found with 7 parameters, I did not have the problem, then I noticed that all of them had been changed to text or select in my desperation to make it show up for placement on the workflow. I returned to 10 parameters, but this time all type="select" and type="text", and everything worked. But slipping even one integer, even with the (optional) min max and default tags, and the tool would disappear on restart. Am I looking at a bug, or is there something I need to be doing to make this tool visible with numeric parameters? MGM

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An error occurred running this job: Args must match #! line at /PATHTOGALAXY/galaxy-central-hbc/tools/filters/fixedValueColumn.pl line 1.
by Robert Chase 09 Apr '12

09 Apr '12

Hello, When we try to add a column to a dataset we get the following error: An error occurred running this job: *Args must match #! line at /share/shared/galaxy-central-hbc/tools/filters/fixedValueColumn.pl line 1. * Perl documentation says this; (F) The setuid emulator requires that the arguments Perl was invoked with match the arguments specified on the #! line. Since some systems impose a one-argument limit on the #! line, try combining switches; for example, turn "-w -U" into "-wU". It works on our development instance without error. -Robert Chase

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Tool Requirement tag and dependency management
by Lance Parsons 09 Apr '12

09 Apr '12

I recently ran into a problem where the tool-dependency env.sh file was not getting sourced for a particular tool. I realized that the problem was in how the tool 'requirement' tag was specified. The requirement tag was specified as in the Tool Config Syntax documentation (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Crequiremen…) <requirements> <requirement type="binary">taxBuilder</requirement> </requirements> However, it appears that the type must be set to "package" in order for the dependency system to source the env.sh file (http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies) <requirements> <requirement type="package">taxBuilder</requirement> </requirements> I'm working on getting this working with bedtools, and I'm wondering what the recommended way to do this would be. Since there are various binaries for this package, I'm thinking I could do something like: <requirements> <requirement type="package">bedtools</requirement> <requirement type="binary">genomeCoverageBed</requirement> </requirements> Secondly, once this is sorted out, it would be nice to update the Tool Config Syntax documentation. Thanks in advance for any advice. -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

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Same error in multiple tools
by Alban Lermine 09 Apr '12

09 Apr '12

Hi, I have the same error message for multiple tools (GFFtoBED, BEDtoBIGBED,BAMtoSAM,...): /from galaxy import eggs ImportError: No module named galaxy It's happening only since the last upgrade, do you know what is going wrong? Thanks, Alban / -- Alban Lermine Unité 900 : Inserm - Mines ParisTech - Institut Curie « Bioinformatics and Computational Systems Biology of Cancer » 11-13 rue Pierre et Marie Curie (1er étage) - 75005 Paris - France Tel : +33 (0) 1 56 24 69 84

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Tasks do not start
by Robert Chase 09 Apr '12

09 Apr '12

Hello, On our test instance of galaxy we have set up filesharing with the rest of our cluster. We have also setup LDAP authentication on the server. We are having problems getting data from the tools based on data_source.py. For instance, if we try to run ucsc main then we can click on "get output" and then "send query to galaxy" we do not get a green screen saying that our task has started, we are redirected right back to the welcome screen. No tasks appear in our history. Has anyone encountered this before? -Rob

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Two questions
by Praveen Raj Somarajan 09 Apr '12

09 Apr '12

Hello, Just want to clarify two questions: 1) Is there a way to get the absolute path of a dataset directly from the interface? This is sometimes useful to create a local directory of all required files (by using symlink) if we know the full path. 2) How do we create a data library from datasets from multiple saved histories? I could see "upload dataset from current history" option in "Add dataset" of DataLibrary, but what is the case if files to be uploaded are distributed in many histories? Do we can another way to accomplish this? Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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MySQL problem at startup
by Federico De Masi 09 Apr '12

09 Apr '12

Derar all, I have recently moved from galaxy-central to galaxy-dist and all seems to work fine except that everytime I start a new session (ie: I go to my galaxy with my browser), I get the error below. I just need to reload the page and all is fine again. I would mention that while the whole 'dist' is original, the ./database/ directory is a mere copy (and updated) of the one I had in galaxy-central. Needless to say that the MySQL engine is never down :) Any help is most than welcome Thanks a million! Here's the error I get. URL: http://galaxy.cbs.dtu.dk/galaxy/ File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 134 in __call__ trans = self.transaction_factory( environ ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 187 in <lambda> self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 207 in transaction_chooser return GalaxyWebUITransaction( environ, galaxy_app, self, session_cookie ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 870 in __init__ self._ensure_valid_session( session_cookie ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 351 in _ensure_valid_session self.app.model.GalaxySession.table.c.is_valid==True ) ) \ File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1300 in first ret = list(self[0:1]) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1221 in __getitem__ return list(res) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1361 in __iter__ return self._execute_and_instances(context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/query.py', line 1364 in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/orm/session.py', line 755 in execute clause, params or {}) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 824 in execute return Connection.executors[c](self, object, multiparams, params) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 874 in _execute_clauseelement return self.__execute_context(context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 896 in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 950 in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File '/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg/sqlalchemy/engine/base.py', line 931 in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) (2006, 'MySQL server has gone away') u'SELECT galaxy_session.id AS galaxy_session_id, galaxy_session.create_time AS galaxy_session_create_time, galaxy_session.update_time AS galaxy_session_update_time, galaxy_session.user_id AS galaxy_session_user_id, galaxy_session.remote_host AS galaxy_session_remote_host, galaxy_session.remote_addr AS galaxy_session_remote_addr, galaxy_session.referer AS galaxy_session_referer, galaxy_session.current_history_id AS galaxy_session_current_history_id, galaxy_session.session_key AS galaxy_session_session_key, galaxy_session.is_valid AS galaxy_session_is_valid, galaxy_session.prev_session_id AS galaxy_session_prev_session_id, galaxy_session.disk_usage AS galaxy_session_disk_usage \nFROM galaxy_session \nWHERE galaxy_session.session_key = %s AND galaxy_session.is_valid = %s \n LIMIT 0, 1' ['ac609feb8dfe0f5669378398dde80af3', 1] -- Federico De Masi, PhD, Assistant Professor The Technical University of Denmark - DTU Center for Biological Sequence Analysis - CBS Kemitorvet 208/002 DK-2800 KGS. LYNGBY, DENMARK Telephone: (+45) 45 25 24 21 Fax: (+45) 45 93 15 85 http://rg.cbs.dtu.dk

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New Tool deployment - Directory of output files
by khanjan gandhi 08 Apr '12

08 Apr '12

Hi there, I am trying to configure a new tool in my instance of galaxy. The tool itself creates a bunch of output files. However, when I run this tool through the galaxy instance, it still creates a folder with all the files in its own directory ( as it does when you run the tool by itself from the command line ). As a results, the output files are not accessible by Galaxy. Is there any way I can configure galaxy to read the entire contents of the output directory or redirect my tool to create the output files in galaxy's default output directory while reading all of them as outputs? Thanks a ton in advance, K

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Problem capturing output from RUM
by Dorset, Daniel C 06 Apr '12

06 Apr '12

I'm writing a wrapper for RUM (RNA-Seq Unified Mapper). For those of you who aren't familiar with RUM, it produces several output files. I'm trying to capture 12 of those files in Galaxy. Here is one of the 12 nodes: <data format="tabular" name="feature_quantifications_galaxy" label="${tool.name} on ${on_string}: Feature Quantifications" /> All 12 nodes have similar syntax. When I try to run RUM from Galaxy, it's obvious that the program is executing properly. The outputs show up as pending until the execution of RUM has completed. However, the output is not being properly captured. All 12 outputs show up as being in the error state, and when I click on the bug icon I see the following in the error report: yes: standard output: Broken pipe yes: write error Those two lines are repeated literally over a hundred times. In the additional output pane beneath the error pane, It shows the output from RUM, which indicates that the tool indeed ran properly. The text is exactly what I would expect to see if I ran the tool from the command line without any problems. So basically, I'm doing something wrong in capturing the output. I have watched the screencast and perused other wrappers, but I'm not sure at this point where I'm going wrong. The full text of the wrapper is pasted below: <tool id="rum_all" name="RUM" version="0.1">  <description>: RNA-Seq Unified Mapping</description> <requirements> <requirement type="package">rum</requirement> </requirements> <command> ##IMPORTANT!!! You will need to change this to correspond to the specific installation path of RUM on your server perl /data/dorsetdc/rum/bin/RUM_runner.pl ##Reference Genome ##IMPORTANT!!! You will need to change this to correspond to the specific installation path of RUM on your server /data/dorsetdc/rum/conf/rum.config_$refgenome ## Inputs. #if $inputs.paired_or_single == "paired": $inputs.left_input,,,$inputs.right_input #else: $inputs.input #end if ##output directory ./ ## Number of CPU cores ##IMPORTANT!!! Make sure you set the max value to something appropriate for your system. See the RUM tool manpage for more details #if $additional_params.use_additional == "yes": $additional_params.num_cores #else: 16 #end if ##data name (static for now) galaxy ## Additional parameters. #if $additional_params.use_additional == "yes": -min_contig_length $additional_params.min_contig_length #if $additional_params.strandspecific == "yes" -strand_specific #end if #if $additional_params.dnamode == "yes" -dnamode #end if #if $additional_params.count_mismatches == "yes" -countmatches #end if #end if </command> <inputs> <conditional name="inputs"> <param name="paired_or_single" type="select" label="Paired or Single-end data?"> <option value="paired">Paired</option> <option value="single">Single</option> </param> <when value="paired"> <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> </when> <when value="single"> <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> </when> </conditional> <param name="refgenome" type="select" label="Select Reference Genome"> <option value="hg19">Human (hg19)</option> <option value="mm9">Mouse (mm9)</option> </param> <conditional name="additional_params"> <param name="use_additional" type="select" label="Use Additional Params?"> <option value="no">No</option> <option value="yes">Yes</option> </param> <when value="no"> </when> <when value="yes"> <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> <param name="num_cores" type="integer" value="16" min="1" max="32" label="Number of Cores to Use" help="Min of 1, max of 32" /> <param name="strandspecific" type="select" label="Are the Data Strand Specific?"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="dnamode" type="select" label="Run in DNA Mode? (Don't map across splice junctions)"> <option value="no">No</option> <option value="yes">Yes</option> </param> <param name="count_mismatches" type="select" label="Report the number of Mismatches?"> <option value="no">No</option> <option value="yes">Yes</option> </param> </when> </conditional> </inputs> <outputs> <data format="tabular" name="feature_quantifications_galaxy" label="${tool.name} on ${on_string}: Feature Quantifications" /> <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" /> <data format="sam" name="RUM.sam" label="${tool.name} on ${on_string}: All Alignments in SAM" /> <data format="bedGraph" name="RUM.cov" label="${tool.name} on ${on_string}: Depth of Coverage for Unique Mappers" /> <data format="bedGraph" name="RUM_NU.cov" label="${tool.name} on ${on_string}: Depth of Coverage for Non-Unique Mappers" /> <data format="bed" name="RUM_Unique" label="${tool.name} on ${on_string}: Unique Mappers" /> <data format="bed" name="RUM_NU" label="${tool.name} on ${on_string}: Non-Unique Mappers" /> <data format="bed" name="junctions_all.bed" label="${tool.name} on ${on_string}: All Junctions" /> <data format="rum" name="junctions_all.rum" label="${tool.name} on ${on_string}: All Junctions in RUM format" /> <data format="bed" name="junctions_high-quality.bed" label="${tool.name} on ${on_string}: All High-Quality Junctions" /> <data format="bed" name="inferred_internal_exons.bed" label="${tool.name} on ${on_string}: Inferred Internal Exons" /> </outputs> <tests> </tests> <help> RUM is an alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. This tool gives a whole lot of output. This tool integration is currently in testing mode. It was written by Dan Dorset in the Vanderbilt GSR. If you have any questions or observe an error, please contact Dan: daniel.dorset(a)vanderbilt.edu More information about the RUM tool is available at the following URL: http://cbil.upenn.edu/RUM/userguide.php </help> </tool>

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