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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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Fix for #104, resubmitting a job when using relative dirs. #105

Closed jasonsydes closed 6 years ago

jasonsydes commented 6 years ago

This is a fix for #104, #16, #51, and addresses one of the comments in #38. This pull request should help many other people be able to resume their jobs. In short, it allows for resuming a job when the job was submitted with a leading "./" on the working directory.

The example on the README page is what is tripping everyone up.

When you try to restart a job that was submitted like this:

bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal

then the replace() call here: can't

newLine.replace(tempPath, oldPath)

can't do its job. It's trying to replace "./work" inside of

/some/long/path/to/work/progressiveAlignment_temp/Anc0/Anc0_experiment.xml

This commit just removes the leading "./" from those paths if they exist, allowing the job to resume correctly.

joelarmstrong commented 6 years ago

Thanks!

jasonsydes commented 6 years ago

Sure thing! Thank you for Progressive Cactus!

Jason

On Sat, Mar 10, 2018 at 1:02 PM, Joel Armstrong notifications@github.com wrote:

Thanks!

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