Install galaxy locally on Windows

Question: Install galaxy locally on Windows - use Docker or VM

5 months ago by

sgadd • 20

sgadd • 20 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 • 378 views

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modified 5 months ago • written 5 months ago by sgadd • 20

5 months ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k 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 COMMENT • link written 5 months ago by Martin Čech ♦♦ 4.9k

5 months ago by

sgadd • 20

sgadd • 20 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 COMMENT • link written 5 months ago by sgadd • 20

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

ADD REPLY • link written 5 months ago by Martin Čech ♦♦ 4.9k

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