Question: Pipeable command to Liftover (UCSC) builds?
1
gravatar for Tafelplankje
3.3 years ago by
Tafelplankje120
Netherlands
Tafelplankje120 wrote:

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. 

 

bash liftover build genome • 1.1k views
ADD COMMENTlink modified 3.3 years ago by RamRS20k • written 3.3 years ago by Tafelplankje120
0
gravatar for RamRS
3.3 years ago by
RamRS20k
Houston, TX
RamRS20k wrote:

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 <().

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by RamRS20k
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