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
On Fri, Oct 14, 2011 at 10:21 AM, Joseph Hargitai
> we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools,
> like fastqc, stopped working. Are there internal links that we possibly
> Is there a way to adjust the installation via a download or update?
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Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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