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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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Configuration failure should clean up the settings directory #128

Closed delagoya closed 12 years ago

delagoya commented 12 years ago

If you start an alignment and there is a configuration option that causes the job to fail (e.g. can't find an index dir) then you should be able to just re-run the command by editing the previous command in the the shell history. E.g. RUM should clean up the settings directory if an align can't even start.

mdelaurentis commented 12 years ago

Angel,

Do you happen to know the sequence of commands that made this happen, and the specific version of RUM? As of v2.0.2_02, we don't actually create the .rum directory until after we make sure we can access the index and check that the command-line arguments are basically ok. So I am not able to reproduce the issue exactly as you described. If I run "rum_runner align ... " in a fresh directory with a bogus "--index" argument, it complains that it can't access the index, and then exits, without creating the .rum directory. There are a couple more checks I can do before we create the .rum directory, but I want to make sure we're looking at the same issue.

delagoya commented 12 years ago

Sorry, I don't know the version. Greg, can you reply to Mike so we can take care of this issue for the pending 2.0.3 release?

-angel

Angel Pizarro Director, ITMAT Bioinformatics Facility

Calendar: http://bit.ly/pizarro-cal

On Tuesday, September 25, 2012 at 11:19 AM, Mike DeLaurentis wrote:

Angel, Do you happen to know the sequence of commands that made this happen, and the specific version of RUM? As of v2.0.2_02, we don't actually create the .rum directory until after we make sure we can access the index and check that the command-line arguments are basically ok. So I am not able to reproduce the issue exactly as you described. If I run "rum_runner align ... " in a fresh directory with a bogus "--index" argument, it complains that it can't access the index, and then exits, without creating the .rum directory. There are a couple more checks I can do before we create the .rum directory, but I want to make sure we're looking at the same issue.

— Reply to this email directly or view it on GitHub (https://github.com/PGFI/rum/issues/128#issuecomment-8858036).

mdelaurentis commented 12 years ago

This should be fixed now. We don't save the configuration until after we check the command line arguments. There are no more hidden files, so removing all the contents of the output directory is sufficient to clear out a job. See also #117.