Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
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 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: > > > > > > myself. Björn Grüning uses - > > > > > > > > > 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 wrote: >> >> >> >> >> >> this works. Thanks. >> >> On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker >> 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 >>> 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 wrote: > > You probably need to set the 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 > 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/ ___ 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/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
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: myself. Björn Grüning uses - 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 wrote: > > > > > > this works. Thanks. > > On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker > 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 >> 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 >>> wrote: You probably need to set the 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 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/ ___ 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/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
this works. Thanks. On Tue, Apr 28, 2015 at 11:51 AM, Dannon Baker 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 > 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 >> wrote: >> >>> You probably need to set the 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 >>> 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/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
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 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 > wrote: > >> You probably need to set the 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 >> 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/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
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 wrote: > You probably need to set the 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 > 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/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
You probably need to set the 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 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/
Re: [galaxy-dev] new tool works correctly but galaxy thinks it failed
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 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/
[galaxy-dev] 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? ___ 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/
