[galaxy-dev] Exit_code not working anymore
Hi all, We have a Galaxy instance that we are regularly keeping up to date following the Galaxy main, so we have the current version (fd4113962c32 commit). For us, since a few updates (unfortunately, I don't know when it started), the exit_code tag is not working anymore. I made the simplest tool to confirm : tool id=tool_to_come name=tool_to_come description/description command interpreter=bash test.sh $input $output /command inputs param name=input type=text value=7 label=Param / /inputs outputs data name=output format=fasta label=Output / /outputs stdio exit_code range=12 level=fatal description=Grave probleme ! / /stdio help **Tool documentation** /help /tool --- #!/bin/bash set -e if [ $1 -ne 10 ]; then exit 12 else echo Yeah ! $2 fi Anyway, it still doesn't work as it used to... Am I the only one to have the problem ? Can you help me ? Cheers, Mathieu (Rennes - France) ___ 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] Exit_code not working anymore
This is a known issue that we have plans to fix. You can follow our progress here: https://trello.com/c/JfB2w1Br Best, J. On Jul 12, 2013, at 6:09 AM, Mathieu Bahin wrote: Hi all, We have a Galaxy instance that we are regularly keeping up to date following the Galaxy main, so we have the current version (fd4113962c32 commit). For us, since a few updates (unfortunately, I don't know when it started), the exit_code tag is not working anymore. I made the simplest tool to confirm : tool id=tool_to_come name=tool_to_come description/description command interpreter=bash test.sh $input $output /command inputs param name=input type=text value=7 label=Param / /inputs outputs data name=output format=fasta label=Output / /outputs stdio exit_code range=12 level=fatal description=Grave probleme ! / /stdio help **Tool documentation** /help /tool --- #!/bin/bash set -e if [ $1 -ne 10 ]; then exit 12 else echo Yeah ! $2 fi Anyway, it still doesn't work as it used to... Am I the only one to have the problem ? Can you help me ? Cheers, Mathieu (Rennes - France) ___ 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/ ___ 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] Exit_code not working anymore
I noticed this was a problem with the transition to setting metadata externally by default. Return code is completely ignored now (always has been when external metadata setting was enabled). Didn't have time to test the patch, but did post link to one in trello some time ago. On a train without wifi so I cannot find the link, can you apply it and test it out? On Jul 12, 2013 5:07 PM, Mathieu Bahin mathieu.ba...@irisa.fr wrote: Hi all, We have a Galaxy instance that we are regularly keeping up to date following the Galaxy main, so we have the current version (fd4113962c32 commit). For us, since a few updates (unfortunately, I don't know when it started), the exit_code tag is not working anymore. I made the simplest tool to confirm : tool id=tool_to_come name=tool_to_come description/description command interpreter=bash test.sh $input $output /command inputs param name=input type=text value=7 label=Param / /inputs outputs data name=output format=fasta label=Output / /outputs stdio exit_code range=12 level=fatal description=Grave probleme ! / /stdio help **Tool documentation** /help /tool --- #!/bin/bash set -e if [ $1 -ne 10 ]; then exit 12 else echo Yeah ! $2 fi Anyway, it still doesn't work as it used to... Am I the only one to have the problem ? Can you help me ? Cheers, Mathieu (Rennes - France) ___ 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/ ___ 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/
