[galaxy-dev] Re : Error executing tool: cannot find 'database'
Hi Hans, Here is my XML file in a simplificated version (no conditionnal parameters) , -i -r and -k are the mandatory arguments of my tool, written in C++: tool id=myTool name=myTool description the description /description command interpreter=C++ /home/myName/work/galaxy-dist/tools/NGStools/myTool -i=${genome_index} -r=${input} -k=${kmer_length} -o=${output_name} /command inputs param name=i type=select label=Genome index option value=Human path/to/Human /option option value=E.coli path/to/Escherichia coli /option /param param format=txt name=r type=data label=Source File help=Select a file/ param format=raw name=r type=data label=Source File help=Select a file/ param format=doc name=r type=data label=Source File help=Select a file/ param format=fastq name=r type=data label=Source File help=Select a file/ param name=kmer_length type=integer min=15 max=150 value=21 label=k-mer length/ param name=o type=text optional=true label=Output name/ /inputs outputs data format=sam name=myTool_outfile label=myTool on ${database.value_label} / /outputs tests test /test /tests help /help /tool /tool Regards, Marine De : Hans-Rudolf Hotz h...@fmi.ch À : Marine Rohmer marine.roh...@yahoo.fr Cc : galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Envoyé le : Mercredi 30 mai 2012 11h42 Objet : Re: [galaxy-dev] Error executing tool: cannot find 'database' Hi Marine Could you please provide the tool definition xml file. Otherwise it is going to be difficult to guess, what is going wrong Regards, Hans On 05/30/2012 11:10 AM, Marine Rohmer wrote: Hi everyone, I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the command, param etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface. However, when I execute my tool, Galaxy says to me : Error executing tool: cannot find 'database' And in my shell, I can see : 127.0.0.1 - - [30/May/2012:10:47:01 +0200] GET /tool_runner?tool_id=myTool HTTP/1.1 200 - http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while attempting tool execution: Traceback (most recent call last): File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line 1345, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line 1661, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File /home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line 333, in execute data.name = fill_template( output.label, context=params ) File /home/myName/work/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'database' 127.0.0.1 - - [30/May/2012:10:47:07 +0200] POST /tool_runner/index HTTP/1.1 200 - http://localhost:8080/tool_runner?tool_id=myTool; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 I'm a beginner in computer sciences, so I can't understand since over 1 week what's happening ... Any idea what's wrong with this ? (I'm using Ubuntu LTS 12.04) All help will be very very appreciated ! Thank you, Marine ___ 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/ De : Hans-Rudolf Hotz h...@fmi.ch À : Marine Rohmer marine.roh...@yahoo.fr Cc : galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Envoyé le : Mercredi 30 mai 2012 11h42 Objet : Re: [galaxy-dev] Error executing tool: cannot find 'database' Hi Marine Could you please provide the tool definition xml file. Otherwise it is going to be difficult to guess, what is going wrong Regards, Hans On 05/30/2012 11:10 AM, Marine Rohmer wrote: Hi everyone, I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the command, param etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface.
Re: [galaxy-dev] Re : Error executing tool: cannot find 'database'
Marine, I think that xml instructs Galaxy to write a command line like: C++ /home/myName/work/galaxy-dist/tools/NGStools/myTool Perhaps try removing 'interpreter=C++' from the command tag - then Galaxy will use: /home/myName/work/galaxy-dist/tools/NGStools/myTool . which is probably more like what you intended? On Wed, May 30, 2012 at 8:32 PM, Marine Rohmer marine.roh...@yahoo.fr wrote: Hi Hans, Here is my XML file in a simplificated version (no conditionnal parameters) , -i -r and -k are the mandatory arguments of my tool, written in C++: tool id=myTool name=myTool description the description /description command interpreter=C++ /home/myName/work/galaxy-dist/tools/NGStools/myTool -i=${genome_index} -r=${input} -k=${kmer_length} -o=${output_name} /command inputs param name=i type=select label=Genome index option value=Human path/to/Human /option option value=E.coli path/to/Escherichia coli /option /param param format=txt name=r type=data label=Source File help=Select a file/ param format=raw name=r type=data label=Source File help=Select a file/ param format=doc name=r type=data label=Source File help=Select a file/ param format=fastq name=r type=data label=Source File help=Select a file/ param name=kmer_length type=integer min=15 max=150 value=21 label=k-mer length/ param name=o type=text optional=true label=Output name/ /inputs outputs data format=sam name=myTool_outfile label=myTool on ${database.value_label} / /outputs tests test /test /tests help /help /tool /tool Regards, Marine De : Hans-Rudolf Hotz h...@fmi.ch À : Marine Rohmer marine.roh...@yahoo.fr Cc : galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Envoyé le : Mercredi 30 mai 2012 11h42 Objet : Re: [galaxy-dev] Error executing tool: cannot find 'database' Hi Marine Could you please provide the tool definition xml file. Otherwise it is going to be difficult to guess, what is going wrong Regards, Hans On 05/30/2012 11:10 AM, Marine Rohmer wrote: Hi everyone, I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the command, param etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface. However, when I execute my tool, Galaxy says to me : Error executing tool: cannot find 'database' And in my shell, I can see : 127.0.0.1 - - [30/May/2012:10:47:01 +0200] GET /tool_runner?tool_id=myTool HTTP/1.1 200 - http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while attempting tool execution: Traceback (most recent call last): File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line 1345, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line 1661, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File /home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line 333, in execute data.name = fill_template( output.label, context=params ) File /home/myName/work/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'database' 127.0.0.1 - - [30/May/2012:10:47:07 +0200] POST /tool_runner/index HTTP/1.1 200 - http://localhost:8080/tool_runner?tool_id=myTool; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 I'm a beginner in computer sciences, so I can't understand since over 1 week what's happening ... Any idea what's wrong with this ? (I'm using Ubuntu LTS 12.04) All help will be very very appreciated ! Thank you, Marine ___ 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/ De : Hans-Rudolf Hotz h...@fmi.ch À : Marine Rohmer marine.roh...@yahoo.fr Cc : galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Envoyé le : Mercredi 30 mai 2012 11h42 Objet : Re: [galaxy-dev] Error executing tool: cannot find 'database' Hi Marine Could you please provide the tool definition xml file.
Re: [galaxy-dev] Re : Error executing tool: cannot find 'database'
Hi Marine In addition to Ross' comment earlier, there are a few points in the xml I think they are wrong or at least I would code them differently - see my comments in between your text below On 05/30/2012 12:32 PM, Marine Rohmer wrote: Hi Hans, Here is my XML file in a simplificated version (no conditionnal parameters) , -i -r and -k are the mandatory arguments of my tool, written in C++: tool id=myTool name=myTool description the description /description command interpreter=C++ /home/myName/work/galaxy-dist/tools/NGStools/myTool -i=${genome_index} -r=${input} -k=${kmer_length} -o=${output_name} /command There is no variable ${genome_index}, ${input},${output_name}. You defined them as: $i, $r, and $o . Hence, I would write: command /home/myName/work/galaxy-dist/tools/NGStools/myTool -i=$i -r=$r -k=$kmer_length -o=$o /commandcd inputs param name=i type=select label=Genome index option value=Human path/to/Human /option option value=E.coli path/to/Escherichia coli /option /param param format=txt name=r type=data label=Source File help=Select a file/ param format=raw name=r type=data label=Source File help=Select a file/ param format=doc name=r type=data label=Source File help=Select a file/ param format=fastq name=r type=data label=Source File help=Select a file/ I would write this in one line: param format=txt,raw,doc,fastq name=r type=data label=Source File help=Select a file/ Also, have you defined the 'raw' and the 'doc' format? param name=kmer_length type=integer min=15 max=150 value=21 label=k-mer length/ param name=o type=text optional=true label=Output name/ /inputs outputs data format=sam name=myTool_outfile label=myTool on ${database.value_label} / /outputs How about: data format=sam name=myTool_outfile label=myTool on $o / tests test /test /tests help /help /tool /tool there is one /tool too much Hope this helps, Hans Regards, Marine *De :* Hans-Rudolf Hotz h...@fmi.ch *À :* Marine Rohmer marine.roh...@yahoo.fr *Cc :* galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu *Envoyé le :* Mercredi 30 mai 2012 11h42 *Objet :* Re: [galaxy-dev] Error executing tool: cannot find 'database' Hi Marine Could you please provide the tool definition xml file. Otherwise it is going to be difficult to guess, what is going wrong Regards, Hans On 05/30/2012 11:10 AM, Marine Rohmer wrote: Hi everyone, I'm trying with all my best to add an NGS tool into my local Galaxy instance. I've added my tool in tool_conf.xml, and made a XML file with all the command, param etc... I think it's pretty ok, and everything is correctly displayed on the Galaxy interface. However, when I execute my tool, Galaxy says to me : Error executing tool: cannot find 'database' And in my shell, I can see : 127.0.0.1 - - [30/May/2012:10:47:01 +0200] GET /tool_runner?tool_id=myTool HTTP/1.1 200 - http://localhost:8080/root/tool_menu; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 galaxy.tools ERROR 2012-05-30 10:47:07,424 Exception caught while attempting tool execution: Traceback (most recent call last): File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line 1345, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File /home/myName/work/galaxy-dist/lib/galaxy/tools/__init__.py, line 1661, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File /home/myName/work/galaxy-dist/lib/galaxy/tools/actions/__init__.py, line 333, in execute data.name = fill_template( output.label, context=params ) File /home/myName/work/galaxy-dist/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /home/myName/work/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File DynamicallyCompiledCheetahTemplate.py, line 83, in respond NotFound: cannot find 'database' 127.0.0.1 - - [30/May/2012:10:47:07 +0200] POST /tool_runner/index HTTP/1.1 200 - http://localhost:8080/tool_runner?tool_id=myTool; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:12.0) Gecko/20100101 Firefox/12.0 I'm a beginner in computer sciences, so I can't understand since over 1 week what's happening ... Any idea what's wrong with this ? (I'm using Ubuntu LTS 12.04) All help will be very very appreciated ! Thank you, Marine ___ 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/