Question: Install galaxy locally on Windows - use Docker or VM
1
gravatar for sgadd
29 days ago by
sgadd20
sgadd20 wrote:

Hello, I do not have access to a Linux/Unix or Mac OS machine, but I occasionally run commands with Git Bash, so I was hoping to be able to install local Galaxy using this method. Is this possible? I will be using clinical data for my analyses and so cannot use the public server. I started the process by downloading the gzip galaxy-master file and running the sh run.sh command, but I got the following error:

$ sh run.sh
Initializing config/migrated_tools_conf.xml from migrated_tools_conf.xml.sample
Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample
Initializing config/shed_tool_data_table_conf.xml from shed_tool_data_table_conf.xml.sample
Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample
Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample
Initializing tool-data/shared/ucsc/manual_builds.txt from manual_builds.txt.sample
Initializing static/welcome.html from welcome.html.sample
Creating Python virtual environment for Galaxy: .venv
To avoid this, use the --no-create-venv flag or set $GALAXY_VIRTUAL_ENV to an
existing environment before starting Galaxy.
Fetching https://pypi.python.org/packages/source/v/virtualenv/virtualenv-13.1.2.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   122  100   122    0     0    458      0 --:--:-- --:--:-- --:--:--   521
Verifying /tmp/galaxy-virtualenv-56IFFn/virtualenv-13.1.2.tar.gz checksum is aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc
Traceback (most recent call last):
  File "<string>", line 1, in <module>
IOError: [Errno 2] No such file or directory: '/tmp/galaxy-virtualenv-56IFFn/virtualenv-13.1.2.tar.gz'

Thanks in advance for any help you can provide. Samantha

windows admin install local galaxy • 126 views
ADD COMMENTlink modified 25 days ago • written 29 days ago by sgadd20
2
gravatar for Martin Čech
29 days ago by
Martin Čech ♦♦ 4.8k
United States
Martin Čech ♦♦ 4.8k wrote:

Galaxy will not run on Windows.

Use the preconfigured Galaxy docker image: https://hub.docker.com/r/bgruening/galaxy-stable/ using Kitematic.

Alternatively you can create a virtual machine (using e.g. VirtualBox) and install e.g. Ubuntu there. Then you can run Galaxy.

ADD COMMENTlink written 29 days ago by Martin Čech ♦♦ 4.8k
1
gravatar for sgadd
25 days ago by
sgadd20
sgadd20 wrote:

Thank you for the replies. I did attempt to use the Docker approach, but unfortunately I ran into issues when I tried to start the page in the local host. So, I finally decided to get a dual boot system with Windows and Ubuntu. I’ve been meaning to do this for a while now since many programs I want to use are not compatible with Windows. After booting into Linux, I was able to set up local Galaxy using the wiki instructions. I’m in no way an expert with Linux, but I found the whole process to be easier than I expected because the instructions were quite clear. Thanks, Samantha

ADD COMMENTlink written 25 days ago by sgadd20

Happy to hear that, thanks for sharing! Let us know if you want our assistance at any point.

ADD REPLYlink written 25 days ago by Martin Čech ♦♦ 4.8k
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