Question: Trouble installing 'Genomic Interval Operations' locally on an Ubuntu VM
1
gravatar for halheinrich
2.7 years ago by
halheinrich10
Canada
halheinrich10 wrote:

​I've successfully set up an Ubuntu VM on VirtualBox. The base Galaxy install seems fine, and I'm set up as an admin. The first two steps, getting data, work fine. But for the third step, the join, I need to add to the tool shed. The tools partially install, but when I run the join, I get this error: ImportError: No module named bx.intervals Going to "Installed tool shed repositories", I see that package_bx_python_0_7 has a status of "Installed, missing tool dependencies". When I uninstall and reinstall this package, I get the following error: Traceback (most recent call last): File& #34;/home/coursera/galaxy-master/dependency_dir/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',& #39;console_scripts', 'pip')() File& #34;/home/coursera/galaxy-master/dependency_dir/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& #34;/home/coursera/galaxy-master/dependency_dir/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& #34;/home/coursera/galaxy-master/dependency_dir/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& #34;/home/coursera/galaxy-master/dependency_dir/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& #34;/home/coursera/galaxy-master/dependency_dir/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 fileInstalled tool dependencies: bx-python Tool shed repository 'package_bx_python_0_7' tool dependencies Name Version Type Status Error bx-python 0.7.1 package Error Traceback (most recent call last): File "/home/coursera/galaxy-master/dependency_dir/bx-python/0.7.1/devteam/package_bx_python_0_7/2d0c08728bca/venv/bin/pip", line 8, in load_entry_point('pip==1.3.1', 'console_scripts', 'pip')() File "/home/coursera/galaxy-master/dependency_dir/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/coursera/galaxy-master/dependency_dir/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/coursera/galaxy-master/dependency_dir/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/coursera/galaxy-master/dependency_dir/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/coursera/galaxy-master/dependency_dir/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 Any help is very much appreciated!

ADD COMMENTlink written 2.7 years ago by halheinrich10

I have exactly the same problem, except that I haven't uninstalled and re-installed the join tool

ADD REPLYlink written 2.7 years ago by jryan4000
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