On Jul 5, 2012, at 9:21 PM, Rob Syme wrote:
> Hi all.
> When I run the FastQC tool using the default local job runner, it produces a
> folder of files with permission 664:
> -rw-rw-r-- 1 galaxy galaxy 17K Jul 5 17:29 duplication_levels.png
> -rw-rw-r-- 1 galaxy galaxy 1.6K Jul 5 17:29 error.png
> -rw-rw-r-- 1 galaxy galaxy 7.5K Jul 5 17:29 fastqc_data.txt
> When I switch to using the(local) pbs queue, it produces a folder with
> permissions 600:
> -rw------- 1 galaxy galaxy 15K Jul 6 09:10 duplication_levels.png
> -rw------- 1 galaxy galaxy 1.6K Jul 6 09:10 error.png
> -rw------- 1 galaxy galaxy 8.8K Jul 6 09:10 fastqc_data.txt
> The final dat file (in database/files/000/dataset_xx.dat) is fine, it's just
> the files in the corresponding folder (database/files/000/dataset_xx_files/*)
> that have the incorrect permissions.
> These more restrictive permissions mean that the files cannot be read by
> apache, resulting a bunch of broken links when viewing the tool's output.
> Does anybody know why this might be happening or how to resolve it?
In your cluster user's .bash_profile, try setting `umask 022` to cause new
files to be created with world-readable permissions.
> Many thanks.
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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: