I was wondering if anyone has trick to make the UCSC LiftOver program pipable in bash? (https://genome.ucsc.edu/cgi-bin/hgLiftOver)
As I understand the application creates files from files, which is quite annoying sometimes; it would be handy if it could use stdin and stdout for the input/output.
1 answer
The link in the bottom of that page gives you a resource where you can download an executable (and other required files) from.
EDIT: I'm assuming you've already downloaded the executable and are looking to bypass the input file creation step. To do this, take a look at process substitution. Essentially, you can feed in your input generator pipeline as a sub-process to the liftOver tool using <().
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