Hi John,

when you say tool autoinstalled via conda do you mean that the dependencies 
were automatically installed during the repository installation process,
or that you have `conda_auto_install = True` in your galaxy.ini ?

The latter is not working reliably while the dependencies have not finished the installation process.
To avoid this you can make sure that the dependency is correctly installed before running the tool
(the dependency in the admin panel -> Manage tool dependencies is green and no conda process is still active).


On 30 January 2018 at 03:15, John Letaw <letaw@ohsu.edu> wrote:

Hi all,


I’m receiving the following error trying to access tools autoinstalled via conda:


Fatal error: Exit code 126 ()

~/galaxy/database/jobs_directory/000/38/tool_script.sh: line 41: ~/galaxy/database/dependencies/_conda/envs/mulled-v1-bb83f93efd111e042823e53ddfa74c32d81ba74cceca9445dfddfc9e940ff738/bin/samtools: Text file busy


So, something is happening too fast I guess, meaning a process is attempting access while this is being created.  Any ideas on how I can diagnose this?  Not seeing any other errors floating around the logs.  Maybe we are dealing with a lustre file locking issue?




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