Ross,
i am looking through three of our instances and none has any jar files in the /shared/jar/ folder.
so it happens, i also cannot bring up a new cloud instance either to verify this issue.
j
________________________________________ From: Ross [ross.lazarus@gmail.com] Sent: Thursday, October 13, 2011 11:19 PM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] moving the galaxy-dist folder structure
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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-- 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;