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?

Many thanks.

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