moving the galaxy-dist folder structure
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
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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;
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
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- 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;
participants (2)
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Joseph Hargitai -
Ross