Question: Can't install galaxy-ops into toolshed
gravatar for njoebott
9 weeks 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 • 86 views
ADD COMMENTlink written 9 weeks 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 12 days ago by njoebott30
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