Running Rnahybrid In Batch

Question

[biolab]

Hi everyone,

I am running RNAhybrid commands for many files using various parameters. I integrated all these RNAhybrid commands in a pipe.sh file and run bash pipe.sh for this task. However, it is low in speed, because it is running RNAhybrid command one afer another. I am wondering how to run these RNAhybrid commands in parallel. Could anyone kindly provide me suggestions and answers? I appreciate your help very much!!

RNAhybrid [parameter 1] input1 > output1
RNAhybrid [parameter 2] input1 > output2
RNAhybrid [parameter 1] input2 > output3
RNAhybrid [parameter 3] input2 > output4
... ...

[Zhaorong]

You may want to take a look at the discussion on SO.

[biolab]

Thanks a lot! Really helpful.

Answer 1

[Biomonika (Noolean)]

Use the commands you are using but add "&" at the end of each.

RNAhybrid [parameter 1] input1 > output1 &
RNAhybrid [parameter 2] input1 > output2 &
RNAhybrid [parameter 1] input2 > output3 &
RNAhybrid [parameter 3] input2 > output4 &

However, without studying deeper you may as well end up overloading the server or being unable to kill the unwanted processes. Least you can do is to remember PID (process ID) you get after running these.

[biolab]

Thank you very much! It is really helpful.