Question: Problem running Galaxy with Cygwin
gravatar for eggrandio
9 months ago by
eggrandio10 wrote:


I am trying to run an instance of Galaxy on my own computer to be able to use the GenometriCorr tool ( but I cannot get it to run. I guess it's more of a problem of my setup than Galaxy, but wanted to ask here in case anyone had found the same error before. Bear in mind I have near zero experience with linux.

I am using Cygwin to run linux on my Windows computer. I was able to use Git to obtain a Galaxy "clone":

$ git clone -b release_17.01
Cloning into 'galaxy'...
remote: Counting objects: 266772, done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 266772 (delta 0), reused 0 (delta 0), pack-reused 266769
Receiving objects: 100% (266772/266772), 206.35 MiB | 572.00 KiB/s, done.
Resolving deltas: 100% (211739/211739), done.
Checking out files: 100% (4418/4418), done.

After that, when I run the $ sh command I obtain the following error:

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 tool-data/shared/ucsc/ucsc_build_sites.txt from ucsc_build_sites.txt.sample
Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample
Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample
Initializing static/welcome.html from welcome.html.sample
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0Warning: Failed to create the file
Warning: /tmp/galaxy-virtualenv-xockOM/virtualenv-13.1.2.tar.gz: No such file
Warning: or directory
  0 1679k    0  1886    0     0   3096      0  0:09:15 --:--:--  0:09:15  3096
curl: (23) Failed writing body (0 != 1886)

It looks like it's not able to download the file. I am able to download the virtualenv-13.1.2.tar.gz file form that address manually but I dont know where to unzip it or how to use it to get my instance of Galaxy running.

Any help is appreciated.

software error galaxy • 239 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by eggrandio10
gravatar for Martin Čech
9 months ago by
Martin Čech ♦♦ 4.3k
United States
Martin Čech ♦♦ 4.3k wrote:

I am not aware of any Cygwin users running Galaxy. Would you consider running a VM with actual Linux instead? You can then try pre-configured Galaxy form this image. Alternatively you could try docker using the Kitematic GUI and using Galaxy Docker image

ADD COMMENTlink written 9 months ago by Martin Čech ♦♦ 4.3k
gravatar for eggrandio
9 months ago by
eggrandio10 wrote:

Hi Martin,

Thanks for your help. I have installed the pre-configured Galaxy from the link you provided.

I am trying to find a way of running the GenometriCorr tool from the VM but I am not able to do it.

I am trying to follow the instructions at:

But I am afraid they are outdated or it does not work from the VM. I cannot find the tool_conf.xml file in the VM.

ADD COMMENTlink written 9 months ago by eggrandio10

Those are very old instructions for an old tool. Also it assumes you have R installed and configured in your environment since there are no requirements specified for the tool so Galaxy wouldn't know what to install for it to run.

Are you sure there is no alternative to using this script? Maybe some other tool from the Tool Shed?

ADD REPLYlink modified 9 months ago • written 9 months ago by Martin Čech ♦♦ 4.3k
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