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kellrott / galaxy-tooldev-docs

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Need more documentation on running tools #4

Closed mjko1210 closed 9 years ago

mjko1210 commented 9 years ago

It took me a while to figure out how to link input data on docker (xml) file.

In DPC example, I indicated input vcf file with <param name="input_vcf" value="mutect_filtered_IS3_chr21.vcf"/> inside of <test>.

Plus, I had to copy the input data into 'test-data' folder by creating a new one which is in the same directory with dpc.xml.

Test was passed.

All 1 test(s) executed passed.

dpc[0]: passed

With job standard output from 'tool_test_output.html': [1] "num.muts=134" [1] 100 [1] 200 [1] 300 [1] 400 [1] 500 [1] 600 [1] 700 [1] 800 [1] 900 [1] 1000 [1] "density.smooth=0.1" [1] "No mutationCopyNumber. Using mutation burden" [1] "highest density is at 0.103326810176125"

I think it run completely without an error but I didn't get other outputs like png and txt files. Do I have to indicate output as well inside of dpc.xml?

Thanks, Minjeong

kellrott commented 9 years ago

Is this from running the planemo unit testing? Because you mention using the tool-data directory, I'm assuming that you followed tool testing instructions? I think the unit testing automatically cleans up and removes the results after a successful test. If you actually want to run the tool and inspect the results, you need to use the web ui.

mjko1210 commented 9 years ago

I chose vagrant based development and followed tool development procedure described in https://www.synapse.org/#!Synapse:syn2786217/wiki/209797. After that, I run tools using planemo --galaxy_root=/path/to/galaxy t. So you didn't cover the section for running tools using the web ui yet? I couldn't find any other option for running tools except that planemo command.

kellrott commented 9 years ago

The assumption was that people would log into the web site once it was launched. I guess a intro chapter about how to use the Galaxy UI needs to be added.

mjko1210 commented 9 years ago

That would be good! Some of people will not be familiar with galaxy UI.

kellrott commented 9 years ago

I've added a new section with links to tutorials and videos from the Galaxy community ( https://www.synapse.org/#!Synapse:syn2786217/wiki/213548 )