New Galaxy User

Question: New Galaxy User

7.5 years ago by

Hi All, I am a new user of Galaxy. I am trying to configure galaxy on my local system. I took clone of repository(https://bitbucket.org/galaxy /galaxy-dist). But I have couple of issues while understanding code base: 1. Is there any help file explaining directory structure and what all configuration files used for? 2. I got list of all dependencies from website, Do I have to install all tools in /usr/local/bin/ or can be installed at any custom location? I have already gone through tutorial (http://gmod.org/wiki/Galaxy_Tutorial) which was quite helpful and interesting but doesn't quite talk about my doubts above. Regards Gaurav Thareja -- Regards Gaurav Thareja

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modified 7.5 years ago by Paul-Michael Agapow • 120 • written 7.5 years ago by gaurav thareja • 30

7.5 years ago by

Louise-AmélieSchmitt • 160

Louise-AmélieSchmitt • 160 wrote:

Hi 1 -> You might want to read the bitbucket wiki instead: https://bitbucket.org/galaxy/galaxy-central/wiki/Home There you can find all the information you will need to understand the configuration files, but don't expect a detailed description of the whole directory structure. The information is divided in topics. It's easier to understand that way anyway. 2 -> If you mean the prerequisites, you might just need an appropriate version of python. (since you already have mercurial) If you mean the software behind each tool, it has to be in the $PATH of the user running Galaxy. If you mean the eggs, Galaxy will do it for you. Hope that helps :) (hopefully I didn't forget anything, lack of sleep is a pain) Regards, L-A Le 16/06/2011 13:14, gaurav thareja a écrit :

ADD COMMENT • link written 7.5 years ago by Louise-AmélieSchmitt • 160

7.5 years ago by

Paul-Michael Agapow • 120

Paul-Michael Agapow • 120 wrote:

Gaurav all The Galaxy wiki is the best place to go for these things, as Louise-Amelie said. You should be able to ignore most things in the config files initially as they will "just work". You can ignore most of the directory structure as well, except perhaps the "tools" directory. all Mostly, the install should (again) "just work" (install the tarball or distrib and run). I've a got a Galaxy installation checklist here: <http: www.agapow.net="" science="" bioinformatics="" galaxy="" installing-="" galaxy=""> It's a bit peculiar to my own situation, but it might give you another point-of-view. Paul Agapow (paul-michael.agapow@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency ********************************************************************** **** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ********************************************************************** ****

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