Running galaxy on external hard drive
Hi, I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can run Galaxy by installing it on an external hard drive. I tried already, and was able to install it properly and connect, but I get errors when I try to upload data. Any help would be greatly appreciated. I don't have a lot of experience with Unix systems, so it might be something easy to solve or impossible to do, I have no idea. Thanks! Alessia
Hi Allessia It is difficult to help you without knowing what kind of error you've got..... What is the error message you get? Regards, Hans On 10/31/2011 03:35 PM, Alessia D wrote:
Hi,
I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can run Galaxy by installing it on an external hard drive. I tried already, and was able to install it properly and connect, but I get errors when I try to upload data.
Any help would be greatly appreciated. I don't have a lot of experience with Unix systems, so it might be something easy to solve or impossible to do, I have no idea.
Thanks!
Alessia
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Hi Hans, Thanks for your reply. The error I am getting is "Can't open folder /media/..." But I guess my question was more in general if I can have Galaxy run from an external drive so that it saves everything on it instead of /home, and if so, how (modifications etc..) Thanks A On Mon, Oct 31, 2011 at 11:25 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Allessia
It is difficult to help you without knowing what kind of error you've got.....
What is the error message you get?
Regards, Hans
On 10/31/2011 03:35 PM, Alessia D wrote:
Hi,
I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can run Galaxy by installing it on an external hard drive. I tried already, and was able to install it properly and connect, but I get errors when I try to upload data.
Any help would be greatly appreciated. I don't have a lot of experience with Unix systems, so it might be something easy to solve or impossible to do, I have no idea.
Thanks!
Alessia
______________________________**_____________________________ 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:
Hi Alessia Well, I am not a linux system expert, but I don't see a reason, why you can't run Galaxy from an external drive as long as it is mounted correctly and you have all the read and write permissions. The basic installation of Galaxy does not need any modification. The configuration files are created when you start the server for the first time with " sh run.sh ". Are you sure, you are using a 'clean' installation? or have you moved it around? I recommend you start again from scratch, following the steps explained on the wiki: http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy Regards, Hans On 10/31/11 10:10 PM, "Alessia D" <ad2405@gmail.com> wrote:
Hi Hans,
Thanks for your reply. The error I am getting is "Can't open folder /media/..." But I guess my question was more in general if I can have Galaxy run from an external drive so that it saves everything on it instead of /home, and if so, how (modifications etc..)
Thanks
A
On Mon, Oct 31, 2011 at 11:25 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
Hi Allessia
It is difficult to help you without knowing what kind of error you've got.....
What is the error message you get?
Regards, Hans
On 10/31/2011 03:35 PM, Alessia D wrote:
Hi,
I am very new to Galaxy and so far have only used the online interface. However, I have an old Unix-running computer and I was hoping to run Galaxy as a local instance. However, the computer has a very small hard drive, that is already half full, so I was wondering if there is any way I can run Galaxy by installing it on an external hard drive. I tried already, and was able to install it properly and connect, but I get errors when I try to upload data.
Any help would be greatly appreciated. I don't have a lot of experience with Unix systems, so it might be something easy to solve or impossible to do, I have no idea.
Thanks!
Alessia
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Excerpts from Hotz, Hans-Rudolf's message of 2011-11-01 09:42:38 +0000:
Well, I am not a linux system expert, but I don't see a reason, why you can't run Galaxy from an external drive as long as it is mounted correctly and you have all the read and write permissions.
Also, if you want galaxy to be installed under your home directory (for example) but have just the dataset files on an external drive, you can modify the "file_path" configuration option in universe_wsgi.ini. Importantly, note that the database and the file_path are interconnected, if you keep your existing database you will need to move files to the new location. The safest thing is to start with a clean Galaxy on the external drive. -- James Taylor, Assistant Professor, Biology / Computer Science, Emory University
participants (4)
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Alessia D -
Hans-Rudolf Hotz -
Hotz, Hans-Rudolf
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James Taylor