BioHPC Cloud:
: User Guide

Instructions for Rocky 9 system.

Section 1. How to use Galaxy web site after the server starts?

Contact support@biohpc.cornell.edu to for file upload/download

Section 2. How to start Galaxy server?

Contact support@biohpc.cornell.edu to start Galaxy server.

### The following instructions are for Cent OS 7 system. ###########

## This guide is for Galaxy docker image bgruening/galaxy-stable version 20.09. Detailed instructions can be found at https://github.com/bgruening/docker-galaxy-stable. (This repository has not been updated since then)

1. Start/restart a galaxy container

export myGalaxyDir=/workdir/$USER/mygalaxy
export galaxyVer=20.09

docker1 run -d -p 8020:80 -p 8022:22 
-v $myGalaxyDir:/export 
-e GALAXY_CONFIG_ALLOW_USER_CREATION=false 
-e GALAXY_CONFIG_BRAND="My Lab" 
bgruening/galaxy-stable:$galaxyVer 

It will take 2-3 minutes to start the galaxy web server. 

2. Config the admin user (When re-starting from the same galaxy directory, you DO NOT need to config again)

• From a web browser, open this page: http://cbsuxxxxx.biohpc.cornell.edu:8020/  (replace cbsuxxxxx with your server name)
• Login as admin user:

• For security purpose, you must change the following settings for the admin user:

1. change admin user email: click "manage information" to change admin user email.
2. Change admin user password: click "change password" to change admin user password.
3. Create a new API key: click "Manage API Key", then click "create new Key"

3. Create new users
From the web site, click "Admin", "Users", "Create new user"

4. As admin user, you can install new tools from galaxy tool shed.

To install new tools, on the web page, click "admin", then in the left panel, click "install new tools" under tool management.

Regular users can use either one of the following three methods to upload data files into Galaxy

1. First method: Upload files from your laptop through web interface: Click "Get data" -> "Upload file" -> "choose local file".

2. Second method: Upload files from your laptop to Galaxy server using filezilla.

Important:

• Login with  user email and password registered with your Galaxy user, not BioHPC user ID;
• Port should be 8022. Not the regular port 22 to upload to the BioHPC server; 

The default directory is: /export/ftp/you_email_address. Once uploaded, you should use the web interface "Get data" -> "Upload file" -> "choose ftp file" to register the files into galaxy

3. Third method: if your data files are already on the BioHPC server, you can copy the data files into galaxy container. Before doing this, you must use the second upload method (upload through Filezilla to port 8022) to upload at least once to have the directory setup properly.

 As the galaxy container has different user permission from your BioHPC server, you do need to take care a few things to copy over files,

#First change the permission of the ftp directory

#get CONTAINER ID
docker1 ps
# replace zzzzzzzz with the container ID you get from the "docker1 ps" command
docker1 exec zzzzzzzz chmod -R a+rwX /export/ftp

#Now you can copy files to the ftp directroy

cp my_DataFiles_Or_Directory  /workdir/$USER/mygalaxy/ftp/my-Email-address

#Important: After copying the files, you need to change the owner of newly copied files to galaxy

docker1 exec zzzzzzzz chown -R galaxy:galaxy /export/ftp

Once done, you need to use the web interface "Get data" -> "Upload file" -> "choose ftp file" to register the uploaded files in galaxy