On Feb 2, 2013, at 1:02 AM, Prasun Dutta wrote:
Hi Nate,
Thanks for the reply. I have already installed VM and downloading Ubuntu now. I had some other queries:
Hi Prasun,
It's best to keep replies on the list, to ensure access to a wide audience of people who may be able to provide better answers than the original respondent.
Can I add my own tools in the main public galaxy? For example, I have some perl scripts that I have to connect together in a workflow. I know, its better to have a local instance for these kind of personal jobs, but still, I would be grateful if you could throw some light on it. And do we have to create our own xml code of the perl program I have written or galaxy can convert it on its own?
It's not possible to install your own tools on Galaxy servers that you don't administrate due to the implications on security and resource usage.
You do need to write your own XML, although for simple tools it is not very difficult and there are a plethora of tutorials and examples available. An automated alternative would be to use the Galaxy Tool Factory:
http://www.ncbi.nlm.nih.gov/pubmed/23024011
--nate
Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK
From: Nate Coraor nate@bx.psu.edu To: Peter Cock p.j.a.cock@googlemail.com Cc: Prasun Dutta prasundutta87@yahoo.co.in; "galaxy-dev@bx.psu.edu" galaxy-dev@bx.psu.edu Sent: Saturday, 2 February 2013 3:11 AM Subject: Re: [galaxy-dev] install Galaxy in Windows (URGENT)
On Feb 1, 2013, at 11:12 AM, Peter Cock wrote:
On Fri, Feb 1, 2013 at 3:48 PM, Prasun Dutta prasundutta87@yahoo.co.in wrote:
Hi Peter,
Unfortunately, I am not an advanced developer in python. Although, I have 'Cygwin' in my system. Any heads up on that will be greatly appreciated?
Cygwin is a useful system for running Unix/Linux tools under Windows, and according to this old email from Nate you would need to use it: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003671.html
More recently a couple of people tried this and ran into problems: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007132.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007180.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007182.html
For the simplest install and maintenance, choose what the Galaxy team use: Linux
Even if you can get the framework to run, many tools with C dependencies are going to be a nightmare to use since the dependencies will almost certainly not compile. The easiest solution these days if you really have no access to a Linux system (the cloud is a good choice here) is probably to install Linux in a VM on your Windows system. This can be done for free with a VM platform like VirtualBox.
--nate
Regards,
Peter ___________________________________________________________ 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: