Peter: GAlaxy is looking for the FastQC executable at the following location (see last line of error message): /opt/galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc You wrote that the fastqc binary is somewhere in Galaxy's $PATH, but is it really in the above directory? If not, try moving the fastqc executable there (or create a symlink) and it should work. Best, Klaus

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