[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:
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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/
