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.laza...@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.hargi...@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;



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