Hi, Joe - not sure this will help but here goes: As you know, most tools expect to find normal executables (like bwa and samtools) on the execution host path but java packages like FastQC are a special case. Java based tool wrappers like the Picard tools expect to find the Picard jar files in [...]/tool-data/shared/jars FastQC is an even more particular case because there's a fastqc perl script which has to be in the same place as the fastqc java, so the Galaxy tool wrapper expects to find it inside a copy of the FastQC distribution inside a folder called [your galaxy root]/tool-data/shared/jars/FastQC. If you moved or recursively copied all of the subdirectories of your Galaxy root from one place to another (including tool-data/shared) everything should just continue to work unless there are permission problems? On Fri, Oct 14, 2011 at 10:21 AM, Joseph Hargitai <joseph.hargitai@einstein.yu.edu> wrote:
Hi,
we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like fastqc, stopped working. Are there internal links that we possibly ignored?
Is there a way to adjust the installation via a download or update?
joe
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