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: <snip> -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 <snip>

When I switch to using the(local) pbs queue, it produces a folder with permissions 600: <snip> -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 <snip>

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?

Hi Rob, In your cluster user's .bash_profile, try setting `umask 022` to cause new files to be created with world-readable permissions. --nate

Many thanks.

-r ___________________________________________________________ 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:

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