Dear sir, madam, I have installed a local copy of Galaxy on my Ubuntu 16.4 computer. This installation went without any problems and Galaxy seemed to work allright. However, I cannot install the tool 'Join the intervals of two datasets side by side', because the installation of the dependent package_bx_python_0_7 repeatedly faills with the errormessage: I/O operation on a closed file. There are two versions of the tool in the Toolshed but they both give the same error. And I have tried to install each version several times. I have followed your guide to the letter and I am certain that I did not make any mistakes. Do you have a solution? Regards, P. Grotendorst
At this point I would try to reinstall the package_bx_python as it seems the installation was interrupted. You can do this from the detail in the top right menu or from 'Manage installed repositories' admin menu.
Reinstalling bx_python did not work. However, I made new environments for Python and Galaxy and tried to install the tool again. It failed several times but this time I could understand the error messages. So I had to load libbz2-dev, libprocps4, procps and sqlite3 and recompile Python again. Finally, all three elements of the tool seemed properly installed because they were all green. But my joy was short lived. The tool produced this error:
Traceback (most recent call last): File "/home/pieter/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/ffbd1de29c28/join/gops_join.py", line 17, in <module> from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped File "/home/pieter/galaxy/lib/galaxy/tools/__init__.py", line 18, in <module> from mako.template import Template ImportError: No module named mako.template
I installed the mysterious module(?) python-mako and recompiled Python for the umptiest time. But I received the same error message. Now I am stuck again. Can somebody please tell me how to resolve this error? I would like to work with Galaxy instead of solving python problems. Regards, Pieter