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precisely / bioinformatics

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Test bootstrapping Docker image from scratch, and document #43

Closed taltman closed 6 years ago

taltman commented 6 years ago

Use the Dockerfile to generate a working image on your laptop. Then, document the way to do it on the README.md file. Thanks!

taltman commented 6 years ago

I'd like you to test that the Dockerfile works correctly to build a Docker image from scratch. Warning, the data download can take a long time, so best to let it run overnight.

mxscott commented 6 years ago

Do you want the Dockerfile to run all the tests automatically by running the Makefile?

taltman commented 6 years ago

The Makefile by default just builds the project (i.e., the 'install' target); it doesn't run tests. The test-running target should be a separate top-level target in the Makefile.

mxscott commented 6 years ago

Another question for you, Tomer: to run my convertAncestry.py file, I use:

'''python convertAncestry.py ancestry_input.txt'''

it runs fine unless I use: 'make test'. In that case I get an error saying:

return compile(source, filename, mode, PyCF_ONLY_AST) File "test/AncestryDNA.txt", line 19 rsid chromosome position allele1 allele2 ^ SyntaxError: invalid syntax make: *** [test] Error 1

Is it trying to compile AncestryDNA.txt for some reason? How do I avoid that?

mxscott commented 6 years ago

Under the test target in the makefile I call: python convertAncestry.py ancestry_input.txt