Manual to install galaxy locally

Question: Manual to install galaxy locally

22 months ago by

I think we need like 10 pages of manual to install galaxy on local machines. The main problem I have is limited space on usegalaxy and inability to install an appropriate copy on the university server. i and many others have the same problems over and over again. I think somebody need to address this issue or galaxy will remain the limited platform instead of the one platform. The main problems I guess that we need to address in this manual are:

Install and run on local machine and on linux server
Admin rights and installing the right tools (with no errors), a working edition of (Hisat, Tophat, Cufflinks...etc) rather than a choice of several edition and packages
Getting to embed Genome sequences (like usegalaxy) and choosing the best annotations
Using FTP programs on local machines and Linux server, including the option to transfer files to special directory using linux command line rather than FTP.

I think it would be a great manual for beginners... Unbelievably useful and important...

Maybe somebody can help?

annotation ftp galaxy install • 1.9k views

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modified 22 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by ruslan.alali • 0

22 months ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

Hi Ruslan

It is difficult to assemble a 'manual' since every local galaxy installation has different requirements in terms of tools and databases and different hardware. Also, it is in the nature of a open source project with such a big developer community, that the documentation is in constant flux (e.g. the current wiki migration). Nevertheless, IMHO, the galaxy documentation is excellent compared to other similar projects.

Let me address your points

"1. Install and run on local machine and on linux server"

https://wiki.galaxyproject.org/Admin/GetGalaxy

https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

"2. Admin rights and installing the right tools (with no errors), a working edition of (Hisat, Tophat, Cufflinks...etc) rather than a choice of several edition and packages"

if you referring to the galaxy admin, see: https://wiki.galaxyproject.org/Admin/Interface

wrt the tools: this depends on your requirements, and I strongly suggest to install only the tools you gonna need

"3. Getting to embed Genome sequences (like usegalaxy) and choosing the best annotations"

again, this depends on your local requirements.

"4. Using FTP programs on local machines and Linux server, including the option to transfer files to special directory using linux command line rather than FTP."

Have a look at the galaxy API: http://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html

You might also wanna look at the slides of the recent galaxy admin training workshop (https://github.com/martenson/dagobah-training ) and at the admin corner of the galaxy training material which is currently being put together (https://github.com/galaxyproject/training-material/tree/master/Admin-Corner )

I hope this helps, otherwise, it is best to ask specific questions in a new thread about a problem you have run into

Regards, Hans-Rudolf

ADD COMMENT • link written 22 months ago by Hotz, Hans-Rudolf • 1.8k

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