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gvlproject / gvl.ansible.playbook

Playbook for building the Genomics Virtual Laboratory
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Summary Statistics tool is missing #52

Open igormakunin opened 8 years ago

igormakunin commented 8 years ago

Statistics > 'Summary Statistics for any numerical column' tool is missing in GVL-4.1.0. The tool: /mnt/galaxy/galaxy-app/tools/stats/gsummary.py

The tool does not work on GVL-4.0.0. The error message says: No module named rpy

madisonkeene commented 8 years ago

Removed completely - doesn't work because of rpy issues

afgane commented 8 years ago

This has been fixed in the ansible-galaxy-cloudman-setup role: https://github.com/galaxyproject/ansible-cloudman-galaxy-setup/pull/7

AndrewIsaac commented 7 years ago

UPDATE: Need to verify if this is still broken in Galaxy-main because it is not in our control

jessicachung commented 7 years ago

Summary Statistics works in Galaxy-main, but is still broken in our current 4.2 dev.

Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/mnt/galaxy/galaxy-app/tools/stats/gsummary.py", line 124, in <module>
    main()
  File "/mnt/galaxy/galaxy-app/tools/stats/gsummary.py", line 65, in main
    tmp_file.write( "%s\n" % hdr_str )
  File "/mnt/galaxy/tools/_conda/envs/__rpy2@2.7.8/lib/python3.5/tempfile.py", line 483, in func_wrapper
    return func(*args, **kwargs)
TypeError: a bytes-like object is required, not 'str'
Slugger70 commented 7 years ago

I use the fact that it is reliably broken in my training workshops.. However, fixing it would be better.. It is one of the tools that comes with Galaxy. We should ask galaxyproject how they fixed it.