Question: Trouble installing a Tool from the Toolshed
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p.grotendorst • 0 wrote:
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
Do you see any error in the Galaxy's log? Where did you see the error you described? How does the installation status look like when you go to 'Manage installed tools'?
I have just installed this tool (https://toolshed.g2.bx.psu.edu/view/devteam/join/ffbd1de29c28) and encountered no problems.
Dear Martin,
The tab 'Manage installed tools' has three entries:
'Join' has a green checkmark, revision ffbd1de29c28, followed by a green panel INSTALLED
'package_bx_python_0_7' has a green checkmark, followed by a gray panel: Installed, missing tool dependencies
'package_galaxy_ops_1-0-0' has a green checkmark, followed by a green panel INSTALLED
The tab 'Tool Error Logs' is empty
By pressing the name 'package_bx_python_0_7' I see that there has been the following error:
Tool shed repository 'package_bx_python_0_7' tool dependencies
bx-python 0.7.1 package Error Traceback (most recent call last): File "/home/pieter/galaxy/database/dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/pip", line 8, in <module> load_entry_point('pip==1.3.1', 'console_scripts', 'pip')() File "/home/pieter/galaxy/database/dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/__init__.py", line 149, in main return command.main(args[1:], options) File "/home/pieter/galaxy/database/dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/basecommand.py", line 181, in main logger.fatal('Storing complete log in %s' % log_fn) File "/home/pieter/galaxy/database/dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/log.py", line 48, in fatal self.log(self.FATAL, msg, args, *kw) File "/home/pieter/galaxy/database/dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/log.py", line 75, in log backwardcompat.fwrite(consumer, rendered) File "/home/pieter/galaxy/database/dependencies/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/local/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/backwardcompat/__init__.py", line 88, in fwrite f.write(s) ValueError: I/O operation on closed file
I understand that something has gone wrong but I don't know the Python language. I hope it makes sense to you. Thanks for your trouble, Pieter Grotendorst