Running Homer programs in the background

Question

[nash.claire]

Hi all,

I'm wondering whether all the Homer users out there know if it's possible to run a Homer perl script in the background on Unix? I'm not that proficient with Unix yet but I've read that you can run programs in the background with "&". Is it possible to run more than one Homer script at the same time? For example, could I run findMotifsGenome.pl on one file at the same time as running annotatePeaks.pl on a different file? Perhaps this is possible with 2 terminal windows open?

[GouthamAtla]

Hello nash.claire!

We believe that this post does not fit the main topic of this site.

`This is not really a bioinformatics question and short answer is` "`Yes`"

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Istvan Albert]

I think this closure is premature in that we really can't expect a newcomer to bioinformatics to understand which question can be answered with unix background and which has bioinformatics relevance. The dividing line IMO is if the tool is a bioinformatics tool or not.

Here the original poster is running a bioinformatics tool and the question that she is asking may even refer to whether the tool makes some changes to files that would preclude it from running it in parallel.

[GouthamAtla]

I thought it's more related to running a tool in the background, but I did not think from other perspective. Thanks.

[nash.claire]

Thank you for the input.

And I apologize if this was the wrong place to ask the question. I posted here as Homer is bioinformatics specific software and wanted to know if it conforms to the same rules as all other perl scripts run through unix. I imagine here is where I'll find people most used to using Homer than anywhere else on the internet.

Back to my question though (if it's still there and if anyone can answer), I know that with Homer I can run the same command on multiple files with the batch function. However, I'm wondering if I can run different commands on different files at the same time. For example, I'm running findMotifsGenome.pl right now and the settings I have to use mean it's going to take quite a long time to complete. However, I have other Homer tasks I want to do on other files so was wondering if I could run those at the same time. Right now my whole terminal is taken up by the findMotifsGenome.pl task so I can't run anything else and it's frustrating........

[Istvan Albert]

just open another terminal - run it there.

Of course in general running two tasks in parallel will make each go slower, the amount of slowdown that depends on many factors, how much memory is used up, how many CPUs the computer has, how much data they read from the disk etc.

Answer 1

[Istvan Albert]

This questions is not strictly bioinformatics oriented, though at the same time deciding which tool or task can be run in parallel depends on the software

Simple unix tools are typically designed to work independently. Other tools (especially bioinformatics tools that don't always use good engineering practices) may have surprising limitations and one needs to be cautious when running them in parallel. For example some tools could use the same temporary file to store intermediate results and that could lead to troubles later on.

In general the answer is that tools can be run in parallel as long as you can isolate them and their effects from one another.