FW: FTP access to Huttenhower Galaxy

[Levesque, Nicole M.]

Hi All,

Think this should be directed to this group.

Thanks,

Nicole

 

From: alyss...@gmail.com [mailto:alyss...@gmail.com] On Behalf Of Alyssa Bost
Sent: Monday, December 01, 2014 10:02 AM
To: Levesque, Nicole M.
Subject: FTP access to Huttenhower Galaxy

 

Good morning,

I am a postdoc in the lab of Angela Douglas at Cornell. I have been trying to access the Huttenhower public instance of Galaxy in order to use the MetaPhlAn tool on out metagenomic datasets, but my files are larger than 2GB and so must be uploaded using the FTP method. I see no FTP address to connect to listed on the upload page, and there is a message that FTP must be enabled by the site administrator. 

Would you be able to help me reach the site administrator so that I could obtain FTP access?

Thank you for you help with this matter.

Alyssa 

 

--

Alyssa Bost, PhD

Laboratory of Angela Douglas

Department of Entomology 

Cornell University

5142 Comstock Hall

Ithaca, NY 14853

 

ab...@cornell.edu

[George Weingart]

Hello Alyssa,

I think that for big files the preferred route is to set up your own instance of Galaxy and then download Metaphlan  from the Galaxy tool-shed.

Here are some sample instructions I prepared some time ago for our team to install a stand-alone instance of Galaxy.

It is very simple and takes ~15 minutes.

Please do not hesitate to contact me if you have further questions, I'll be happy to help.

Best regards,

George Weingart, PhD

Huttenhower Lab

===========================================================================================================

Setting up a new galaxy environment

in a Mac or a VM:

The process takes just a few minutes to complete.

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

Instructions:

1. Clone galaxy:  In the Home directory enter:

hg clone https://bitbucket.org/galaxy/galaxy-dist/

2. Bring to current - Enter the following commands:

cd galaxy-dist
hg update stable

3. Start Galaxy for the first time (It will have to be started twice - see instructions below) - Enter the following command:

bash -l -c 'nohup   sh ~/galaxy-dist/run.sh >> ~/galaxy-dist/galaxy.log &'

4. Verify that Galaxy came up:  Go to a browser and open

http://localhost:8080/

5. Kill Galaxy:  

Enter the following command:  ps -ef|grep paster

The result looks similar to this:  Find the task number

ubuntu@ubuntu-VirtualBox:~/galaxy-dist$ ps -ef|grep paster

ubuntu    2508  2399 12 00:45 pts/0    00:01:12 python ./scripts/paster.py serve universe_wsgi.ini

ubuntu    2791  2197  0 00:55 pts/0    00:00:00 grep --color=auto paster

ubuntu@ubuntu-VirtualBox:~/galaxy-dist$

Kill the task:  - Enter the following command

kill -term 2508

5. Update Galaxy adding yourself as an Admin by updating the member

universe_wsgi.ini

Modify #admin_users = None   (Around line 642)

adding your email, for example:

admin_users = youremail....@gmail.com

6. Update Galaxy   updating the member tool_sheds_conf.xml  so that http  changes to https (Add the “s”)  should look as follows:

<tool_sheds>

   <tool_shed name="Galaxy main tool shed" url="https://toolshed.g2.bx.psu.edu/"/>

   <tool_shed name="Galaxy test tool shed" url="https://testtoolshed.g2.bx.psu.edu/"/>

</tool_sheds>

8. Restart Galaxy - Enter the command:

bash -l -c 'nohup   sh ~/galaxy-dist/run.sh >> ~/galaxy-dist/galaxy.log &'

9. Login to Galaxy, and add yourself as a user

10. You’re good to go!!  Can start downloading applications from the tool shed by using the “Admin” tab in Galaxy and there “Search and Browse Tool-Sheds”

In your particular case - look for Metaphlan.  It is there

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