new tool works correctly but galaxy thinks it failed
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded. How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
Hey Ryan, Yes, this is exactly why. By default, galaxy expects that anything written to stderr means that there was a failure, though you can change this by using the error_code syntax (among other options) found here: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax -Dannon On Tue, Apr 28, 2015 at 11:41 AM Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why? ___________________________________________________________ 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: https://lists.galaxyproject.org/
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You probably need to set the <stdio> tag, since due to a historical design choice by default any output on stderr is treated as an error. See: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Peter On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
___________________________________________________________ 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: https://lists.galaxyproject.org/
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ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly. On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
You probably need to set the <stdio> tag, since due to a historical design choice by default any output on stderr is treated as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly. If yours does, you can set exit_code tags and everything should work. On Tue, Apr 28, 2015 at 11:47 AM Ryan G <ngsbioinformatics@gmail.com> wrote:
ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.
On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
You probably need to set the <stdio> tag, since due to a historical design choice by default any output on stderr is treated as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
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<stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio> this works. Thanks. On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly. If yours does, you can set exit_code tags and everything should work.
On Tue, Apr 28, 2015 at 11:47 AM Ryan G <ngsbioinformatics@gmail.com> wrote:
ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.
On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
You probably need to set the <stdio> tag, since due to a historical design choice by default any output on stderr is treated as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
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I feel like that stdio tag is going to cause it to always pass - even if the exit code is not 0. Am I wrong? I like: <stdio> <exit_code range="1:" /> </stdio> myself. Björn Grüning uses - <stdio> <exit_code range="1:" /> <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> </stdio> which is a popular choice. As a heads up for people reading discussion in the future - starting in 15.05 - you will be able to just add detect_errors="exit_code" on the command tag to get a more sensible default behavior. https://github.com/galaxyproject/galaxy/pull/117 -John On Tue, Apr 28, 2015 at 12:12 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
<stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>
this works. Thanks.
On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly. If yours does, you can set exit_code tags and everything should work.
On Tue, Apr 28, 2015 at 11:47 AM Ryan G <ngsbioinformatics@gmail.com> wrote:
ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.
On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
You probably need to set the <stdio> tag, since due to a historical design choice by default any output on stderr is treated as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
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___________________________________________________________ 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: https://lists.galaxyproject.org/
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You are correct. It's always passing even when it fails. There was nothing in the docs to indicate a pass. Sent from my iPhone
On Apr 28, 2015, at 3:44 PM, John Chilton <jmchilton@gmail.com> wrote:
I feel like that stdio tag is going to cause it to always pass - even if the exit code is not 0. Am I wrong? I like:
<stdio> <exit_code range="1:" /> </stdio>
myself. Björn Grüning uses -
<stdio> <exit_code range="1:" /> <exit_code range=":-1" /> <regex match="Error:" /> <regex match="Exception:" /> </stdio>
which is a popular choice.
As a heads up for people reading discussion in the future - starting in 15.05 - you will be able to just add detect_errors="exit_code" on the command tag to get a more sensible default behavior. https://github.com/galaxyproject/galaxy/pull/117
-John
On Tue, Apr 28, 2015 at 12:12 PM, Ryan G <ngsbioinformatics@gmail.com> wrote: <stdio> <exit_code range="-1" level="fatal" description="RandomSubFq failed" /> </stdio>
this works. Thanks.
On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker <dannon.baker@gmail.com> wrote:
Like Peter mentions, we did this because historically not all tools used (still don't, I guess) exit codes correctly. If yours does, you can set exit_code tags and everything should work.
On Tue, Apr 28, 2015 at 11:47 AM Ryan G <ngsbioinformatics@gmail.com> wrote:
ok, thanks. Let me look at this. When I look at the information about the tool, Galaxy does see the exit code is 0, which I think would be sufficient to know the tool ran correctly.
On Tue, Apr 28, 2015 at 11:45 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
You probably need to set the <stdio> tag, since due to a historical design choice by default any output on stderr is treated as an error. See:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Peter
On Tue, Apr 28, 2015 at 4:41 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:
Hi - I implemented a tool I us into Galaxy but when I run the tool view Galaxy, Galaxy thinks the tool failed. I checked the output file the tools create, and it succeeded.
How do I tell Galaxy that a tool it ran was successful? Is it something in my XML file? The tool is outputting some info to stderr. Could this be why?
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi All, I am relatively new to galaxy and recently had to take over the work on several tools. After the last galaxy update, one of them stopped working. Old working code: <repeat name="pref" title="Select column name preference"> <param name="columntype" type="select" label="Column name" refresh_on_change="true" dynamic_options='filter_column2(library_file, col_type, polarity)' /> </repeat> This worked perfectly, but now, the select shows me "no options available" When i move the param-tag out of the repeat block, it works again. Also, when i put this param within a conditional like: <conditional name="col_pref"> <param name="apply_select" type="boolean" checked="false" label="Select column name preference?" /> <when value="true"> <param name="columntype" type="select" label="Column name" refresh_on_change="true" dynamic_options='filter_column2(library_file,col_type,polarity)'/> </when> <when value="false"> <param name="model" type="hidden" value="False" /> </when> </conditional> the dynamic_options also does not work. I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-w... This seems to be my problem too. Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround. Thank you, Linda Bakker -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
Hey Linda, This seems to be an issue which has already been fixed. Could you please update your instance and/or let me know at which commit it is? Thank you, Aysam On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker <linda.bakker@wur.nl> wrote:
Hi All,
I am relatively new to galaxy and recently had to take over the work on several tools. After the last galaxy update, one of them stopped working.
Old working code:
<repeat name="pref" title="Select column name preference"> <param name="columntype" type="select" label="Column name" refresh_on_change="true" dynamic_options='filter_column2(library_file, col_type, polarity)' /> </repeat>
This worked perfectly, but now, the select shows me "no options available" When i move the param-tag out of the repeat block, it works again. Also, when i put this param within a conditional like:
<conditional name="col_pref"> <param name="apply_select" type="boolean" checked="false" label="Select column name preference?" /> <when value="true"> <param name="columntype" type="select" label="Column name" refresh_on_change="true" dynamic_options='filter_column2(library_file,col_type,polarity)'/> </when> <when value="false"> <param name="model" type="hidden" value="False" /> </when> </conditional>
the dynamic_options also does not work. I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-w... This seems to be my problem too.
Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround.
Thank you,
Linda Bakker
-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Thanks for your reply, I updated my instance and indeed it was fixed! I will update more frequently! Linda On 04/30/2015 03:29 PM, Aysam Guerler wrote:
Hey Linda,
This seems to be an issue which has already been fixed. Could you please update your instance and/or let me know at which commit it is?
Thank you, Aysam
On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker <linda.bakker@wur.nl <mailto:linda.bakker@wur.nl>> wrote:
Hi All,
I am relatively new to galaxy and recently had to take over the work on several tools. After the last galaxy update, one of them stopped working.
Old working code:
<repeat name="pref" title="Select column name preference"> <param name="columntype" type="select" label="Column name" refresh_on_change="true" dynamic_options='filter_column2(library_file, col_type, polarity)' /> </repeat>
This worked perfectly, but now, the select shows me "no options available" When i move the param-tag out of the repeat block, it works again. Also, when i put this param within a conditional like:
<conditional name="col_pref"> <param name="apply_select" type="boolean" checked="false" label="Select column name preference?" /> <when value="true"> <param name="columntype" type="select" label="Column name" refresh_on_change="true" dynamic_options='filter_column2(library_file,col_type,polarity)'/> </when> <when value="false"> <param name="model" type="hidden" value="False" /> </when> </conditional>
the dynamic_options also does not work. I found a trello -bug report: https://trello.com/c/UJKGsWSu/2469-dynamic-options-in-select-fields-do-not-w... This seems to be my problem too.
Can someone confirm for me that it is not possible to use the dynamic_options from within a repeat or conditional block, or am i missing something? Otherwise i have to come up with some sort of workaround.
Thank you,
Linda Bakker
-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 <tel:%2B31-317-480756> email: linda.bakker@wur.nl <mailto:linda.bakker@wur.nl>
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bakker@wur.nl
participants (6)
-
Aysam Guerler -
Dannon Baker -
John Chilton -
Linda Bakker -
Peter Cock -
Ryan G