I am trying to run an instance of Galaxy on my own computer to be able to use the GenometriCorr tool (http://genometricorr.sourceforge.net/galaxy/galaxyintegration.html) 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 https://github.com/galaxyproject/galaxy.git 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 run.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 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 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.