Question: Can't install galaxy-ops into toolshed
gravatar for njoebott
21 months ago by
njoebott30 wrote:

Greetings Galaxy experts and enthusiasts,

I have a simple single node installation of Galaxy using Ubuntu 16.04.1 and python 2.7.12

I Want to perform a simple join operation (per the 101 tutorial) but cannot fully install the dependencies required: package_galaxy_ops_1_0_0 -> galaxy-ops

This is due to a SSL issue because the external location for this package is behind an https and NOT http:

"Error downloading from URL urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:590)"

I was able to download the package, gops-1.0-st.tgz with an external browser and tried to install it in the specified directory, to no avail:


So, I am asking the community here how to proceed with:

  1. Installing the package without the SSL issue. Where can I modify the python code to skip the ssl validation? or,
  2. How can I manually install this package and have Galaxy accept it?

Thanks for any guidance here.

galaxy • 633 views
ADD COMMENTlink written 21 months ago by njoebott30

I am following-up on my inquiry above. Also, where can I find all of the process and/or error messages that are associated with trying to install tools? That is, where can I find the file location where following errors are stored that are present from the GUI:

File "/home/galaxy/galaxy/lib/tool_shed/galaxy_install/", line 121, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/home/galaxy/galaxy/lib/tool_shed/galaxy_install/", line 79, in install_and_build_package initial_download=True ) File "/home/galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 31, in execute_step initial_download=initial_download ) File "/home/galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 665, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/galaxy/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/", line 165, in url_download raise Exception( err_msg )

Error downloading from URL : <urlopen error="" [ssl:="" certificate_verify_failed]="" certificate="" verify="" failed="" (_ssl.c:590)&gt;<="" p="">

ADD REPLYlink written 19 months ago by njoebott30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour