Re: [galaxy-dev] Tool Errors
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 wrote: > On Fri, Sep 12, 2014 at 4:11 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. > > 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 > tag. I think you need to remove the extra spaces to have: > > #if ... > > Not: > > # if ... > > Then it might work? > > Peter > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Errors
On Fri, Sep 12, 2014 at 4:11 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. 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 tag. I think you need to remove the extra spaces to have: #if ... Not: # if ... Then it might work? Peter ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Errors
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:
# 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
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_set
Hope this helps
Hans-Rudolf
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Re: [galaxy-dev] Tool Errors
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 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
>> 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:
Classify with Quikr
# 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
Pretrained
databases
Custom trained quikr database
>>> label="custom
trained database"/>
5
Green Genes
91%
Green Genes
94%
RDP Trained
Set
5
6
7
8
>>> label="lambda" help="default 1"/>
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>>
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Re: [galaxy-dev] Tool Errors
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 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:
Classify with Quikr
# 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
Pretrained
databases
Custom trained quikr database
5
Green Genes
91%
Green Genes
94%
RDP Trained
Set
5
6
7
8
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Re: [galaxy-dev] Tool Errors
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 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:
>>
>>
>>Classify with Quikr
>>
>>
>># 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
>>
>>
>>
>>
>>
>>
>>Pretrained
>> databases
>>Custom trained quikr database
>>
>>
>>
>>
>> 5
>>
>>
>>
>>
>> Green Genes
>> 91%
>> Green Genes
>> 94%
>> RDP Trained
>> Set
>>
>>
>> 5
>> 6
>> 7
>> 8
>>
>>
>>
>> > label="lambda" help="default 1"/>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ___
>> 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/
>>
>> To search Galaxy mailing lists use the unified search at:
>>http://galaxyproject.org/search/mailinglists/
>>
>>
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Re: [galaxy-dev] Tool Errors
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:
Classify with Quikr
# 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
Pretrained
databases
Custom trained quikr database
5
Green Genes 91%
Green Genes 94%
RDP Trained Set
5
6
7
8
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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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