Hi guys, I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means? Thank you, Calvin my xml file: <tool id="quikr" name="Quikr"> <description>Classify with Quikr</description> <command> # if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o ${output} # end if </command> <inputs> <param name="input" type="data" format="fasta" label="input fasta file"/> <conditional name="qdb"> <param name="dbtype" type="select" label="Genomes to score against"> <option value="default" selected="true">Pretrained databases</option> <option value="user">Custom trained quikr database</option> </param> <when value="user"> <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> <param name="dbsize" type="hidden" label="mer size"> <option value="5">5</option> </param> </when> <when value="default"> <param name="dbname" type="select" label="Choose database"> <option value="/data/galaxy/data/gg91">Green Genes 91%</option> <option value="/data/galaxy/data/gg94">Green Genes 94%</option> <option value="/data/galaxy/data/rdp">RDP Trained Set</option> </param> <param name="dbsize" type="select" label="mer size"> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> </when> </conditional> <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <help> </help> </tool>
Hi, as far as I know, it just means your tool did not produced any output, so your results is empty. Nothing more. This is no error, or? The box is not red? Cheers, Bjoern Am 12.09.2014 um 16:28 schrieb Calvin Morrison:
Hi guys,
I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means?
Thank you, Calvin
my xml file:
<tool id="quikr" name="Quikr"> <description>Classify with Quikr</description> <command>
# if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o ${output} # end if
</command> <inputs> <param name="input" type="data" format="fasta" label="input fasta file"/> <conditional name="qdb"> <param name="dbtype" type="select" label="Genomes to score against"> <option value="default" selected="true">Pretrained databases</option> <option value="user">Custom trained quikr database</option> </param> <when value="user"> <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> <param name="dbsize" type="hidden" label="mer size"> <option value="5">5</option> </param> </when> <when value="default"> <param name="dbname" type="select" label="Choose database"> <option value="/data/galaxy/data/gg91">Green Genes 91%</option> <option value="/data/galaxy/data/gg94">Green Genes 94%</option> <option value="/data/galaxy/data/rdp">RDP Trained Set</option> </param> <param name="dbsize" type="select" label="mer size"> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> </when> </conditional> <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <help> </help> </tool>
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Which me thinks is weird, because my code, when given the -v flag will at least put out some info to stdout, or worse case, some errors to stderr, but those are empty too! On 12 September 2014 10:31, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
as far as I know, it just means your tool did not produced any output, so your results is empty. Nothing more. This is no error, or? The box is not red?
Cheers, Bjoern
Am 12.09.2014 um 16:28 schrieb Calvin Morrison:
Hi guys,
I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means?
Thank you, Calvin
my xml file:
<tool id="quikr" name="Quikr"> <description>Classify with Quikr</description> <command>
# if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o ${output} # end if
</command> <inputs> <param name="input" type="data" format="fasta" label="input fasta file"/> <conditional name="qdb"> <param name="dbtype" type="select" label="Genomes to score against"> <option value="default" selected="true">Pretrained databases</option> <option value="user">Custom trained quikr database</option> </param> <when value="user"> <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> <param name="dbsize" type="hidden" label="mer size"> <option value="5">5</option> </param> </when> <when value="default"> <param name="dbname" type="select" label="Choose database"> <option value="/data/galaxy/data/gg91">Green Genes 91%</option> <option value="/data/galaxy/data/gg94">Green Genes 94%</option> <option value="/data/galaxy/data/rdp">RDP Trained Set</option> </param> <param name="dbsize" type="select" label="mer size"> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> </when> </conditional> <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <help> </help> </tool>
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You can check the stderr and stdout in the information (small i Icon) site on every dataset. Also can you see what the log is saying? It should provide you the actuall commandline call, which is produced by the wrapper. Cheers, Bjoern Am 12.09.2014 um 16:33 schrieb Calvin Morrison:
Which me thinks is weird, because my code, when given the -v flag will at least put out some info to stdout, or worse case, some errors to stderr, but those are empty too!
On 12 September 2014 10:31, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
as far as I know, it just means your tool did not produced any output, so your results is empty. Nothing more. This is no error, or? The box is not red?
Cheers, Bjoern
Am 12.09.2014 um 16:28 schrieb Calvin Morrison:
Hi guys,
I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means?
Thank you, Calvin
my xml file:
<tool id="quikr" name="Quikr"> <description>Classify with Quikr</description> <command>
# if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o ${output} # end if
</command> <inputs> <param name="input" type="data" format="fasta" label="input fasta file"/> <conditional name="qdb"> <param name="dbtype" type="select" label="Genomes to score against"> <option value="default" selected="true">Pretrained databases</option> <option value="user">Custom trained quikr database</option> </param> <when value="user"> <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> <param name="dbsize" type="hidden" label="mer size"> <option value="5">5</option> </param> </when> <when value="default"> <param name="dbname" type="select" label="Choose database"> <option value="/data/galaxy/data/gg91">Green Genes 91%</option> <option value="/data/galaxy/data/gg94">Green Genes 94%</option> <option value="/data/galaxy/data/rdp">RDP Trained Set</option> </param> <param name="dbsize" type="select" label="mer size"> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> </when> </conditional> <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <help> </help> </tool>
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The stderr and stdout is empty, according to galaxy. here is paster.log output for quikr when i run it. galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # else quikr -v -k 0 -s "/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # end if that doesn't really seem all that helpful though. On 12 September 2014 10:37, Björn Grüning <bjoern.gruening@gmail.com> wrote:
You can check the stderr and stdout in the information (small i Icon) site on every dataset. Also can you see what the log is saying? It should provide you the actuall commandline call, which is produced by the wrapper.
Cheers, Bjoern
Am 12.09.2014 um 16:33 schrieb Calvin Morrison:
Which me thinks is weird, because my code, when given the -v flag will at
least put out some info to stdout, or worse case, some errors to stderr, but those are empty too!
On 12 September 2014 10:31, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi,
as far as I know, it just means your tool did not produced any output, so your results is empty. Nothing more. This is no error, or? The box is not red?
Cheers, Bjoern
Am 12.09.2014 um 16:28 schrieb Calvin Morrison:
Hi guys,
I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means?
Thank you, Calvin
my xml file:
<tool id="quikr" name="Quikr"> <description>Classify with Quikr</description> <command>
# if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".mat.gz -i ${input} -o ${output} # end if
</command> <inputs> <param name="input" type="data" format="fasta" label="input fasta file"/> <conditional name="qdb"> <param name="dbtype" type="select" label="Genomes to score against"> <option value="default" selected="true">Pretrained databases</option> <option value="user">Custom trained quikr database</option> </param> <when value="user"> <param name="dbname" type="data" format="quikrdb" label="custom trained database"/> <param name="dbsize" type="hidden" label="mer size"> <option value="5">5</option> </param> </when> <when value="default"> <param name="dbname" type="select" label="Choose database"> <option value="/data/galaxy/data/gg91">Green Genes 91%</option> <option value="/data/galaxy/data/gg94">Green Genes 94%</option> <option value="/data/galaxy/data/rdp">RDP Trained Set</option> </param> <param name="dbsize" type="select" label="mer size"> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> </param> </when> </conditional> <param name="lambda" type="integer" size="6" value="10000" label="lambda" help="default 10000"/> </inputs> <outputs> <data name="output" format="tabular" /> </outputs> <help> </help> </tool>
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On 09/12/2014 05:11 PM, Calvin Morrison wrote:
The stderr and stdout is empty, according to galaxy.
here is paster.log output for quikr when i run it.
galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # else quikr -v -k 0 -s "/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # end if
that doesn't really seem all that helpful though.
Actually, it is very helpful, isn't-t? It shows that the command tag from your xml file is not properly executed.
my xml file:
<command>
# if $qdb.dbtype == "user" quikr -v -k 0 -s ${qdb.dbname} -i ${input} -o ${output} # else quikr -v -k 0 -s "${qdb.dbname}${qdb.dbsize}".__mat.gz -i ${input} -o ${output} # end if
</command>
try removing the spaces between "#" and "if", "#" and "else", and "#" and "end if". And re-load the tool configuration. See also: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cwhen.3E_tag_... Hope this helps Hans-Rudolf
On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison <mutantturkey@gmail.com> wrote:
The stderr and stdout is empty, according to galaxy.
here is paster.log output for quikr when i run it.
galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # else quikr -v -k 0 -s "/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # end if
that doesn't really seem all that helpful though.
It does help - that command isn't going to work at the shell - try it and see? The problem is your Cheetah if statement has not been processed, and I think it is as simple as you've used invalid syntax in your <command> tag. I think you need to remove the extra spaces to have: #if ... Not: # if ... Then it might work? Peter
Yes, it seems that has solved the problem! I knew it was something silly. thank you all On 12 September 2014 11:37, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison <mutantturkey@gmail.com> wrote:
The stderr and stdout is empty, according to galaxy.
here is paster.log output for quikr when i run it.
galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # else quikr -v -k 0 -s "/data/galaxy/galaxy-dist/database/files/000/dataset_103.dat".mat.gz -i /data/galaxy/galaxy-dist/database/files/000/dataset_55.dat -o /data/galaxy/galaxy-dist/database/files/000/dataset_104.dat # end if
that doesn't really seem all that helpful though.
It does help - that command isn't going to work at the shell - try it and see?
The problem is your Cheetah if statement has not been processed, and I think it is as simple as you've used invalid syntax in your <command> tag. I think you need to remove the extra spaces to have:
#if ...
Not:
# if ...
Then it might work?
Peter
participants (4)
-
Björn Grüning -
Calvin Morrison -
Hans-Rudolf Hotz -
Peter Cock