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)
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.bahin@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)
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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/
participants (3)
-
Jeremy Goecks -
John Chilton -
Mathieu Bahin