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docker run example in README does not work for me #51

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mccalluc opened this issue Apr 12, 2019 · 0 comments
Open

docker run example in README does not work for me #51

mccalluc opened this issue Apr 12, 2019 · 0 comments

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@mccalluc
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(clodius) clodius$ curl https://raw.githubusercontent.com/hms-dbmi/clodius/develop/test/sample_data/geneAnnotationsExonsUnions.short.bed \
   > /tmp/clodius/input/sample.short.bed

(clodius) clodius$ docker stop clodius
Error response from daemon: No such container: clodius

(clodius) clodius$ docker pull gehlenborglab/clodius
Using default tag: latest
latest: Pulling from gehlenborglab/clodius
....
Digest: sha256:69c09cc20bdfa0d102a7888d502713a9cd0e16fb9637250dd5f6bdb3dc5c1ef3
Status: Downloaded newer image for gehlenborglab/clodius:latest

(clodius) clodius$ docker run -v /tmp/clodius/input:/tmp/ \
>            gehlenborglab/clodius \
>            clodius aggregate bigwig /tmp/file.bigwig
Traceback (most recent call last):
  File "/usr/local/bin/clodius", line 11, in <module>
    load_entry_point('clodius==0.9.4', 'console_scripts', 'clodius')()
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/lib/python2.7/dist-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "build/bdist.linux-x86_64/egg/clodius/cli/aggregate.py", line 1372, in bigwig
NameError: global name '_bigwig' is not defined
mccalluc added a commit that referenced this issue Apr 12, 2019
mccalluc added a commit that referenced this issue Apr 18, 2019
* Syntax highlighting on bash snippets (grey comments)

* typo: "tests" -> "test"

* Running tests created these, but probably should not be committed?

* Does not seem like it could actually write to output before.
(Docker does not actually run for me: #51)

* Rename to take advantage of MD rendering

* link to examples
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