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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
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/
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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/
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/
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
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/
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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-work-in-repeats 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/
galaxy-dev@lists.galaxyproject.org
-
Aysam Guerler -
Dannon Baker -
John Chilton -
Linda Bakker -
Peter Cock -
Ryan G