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? Many thanks. -r
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