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cole-trapnell-lab / cufflinks

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Move cuffcompare temp files out of working dir in cuffmerge #39

Closed xrobin closed 7 years ago

xrobin commented 9 years ago

I was running multiple instances of cuffmerge in the same working directory and all but one exited with the following error:

IOError: [Errno 2] No such file or directory: 'tmp_meta_asm.combined.gtf'

It appears that the calls to cuffcompare within cuffmerge are using temporary files with static names in the working directory, and the file had been moved by one of the processes (the one that succeeded).

This pull request fixes this issue by using tmp_dir instead of tmp_meta_asm.

xrobin commented 9 years ago

Note that I just realized that this problem was already discussed in issue #33.