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ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions
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option to specify port for blat #9

Closed jasper1918 closed 9 years ago

jasper1918 commented 9 years ago

Hi,

Congrats on putting together a great program for fusion detection.

I have been using breakmer on a server where the default option of blat 8000-9500 will not work because they are occupied or at least the random port is routinely hitting an occupied port. Any chance you can add an option to specify the port number?

Thanks!

-Jeff

ryanabo commented 9 years ago

Hi Jeff,

Thanks for testing and using BreaKmer. I have added this feature in the master branch. You will just need to include the following in your configuration file:

'blat_port='

I have not tested it yet, so please let me know if it works (or not).

Ryan

jasper1918 commented 9 years ago

I'll give it a try and let you know. Thanks for the quick fix!!

-Jeff

On Friday, May 15, 2015, Ryan Abo notifications@github.com wrote:

Hi Jeff,

Thanks for testing and using BreaKmer. I have added this feature in the master branch. You will just need to include the following in your configuration file:

'blat_port='

I have not tested it yet, so please let me know if it works (or not).

Ryan

— Reply to this email directly or view it on GitHub https://github.com/a-bioinformatician/BreaKmer/issues/9#issuecomment-102553773 .

Jeff Jasper (801) 372-2395

jasper1918 commented 9 years ago

Its been awhile but just noticed this was left open. The fix worked as expected. Thanks!!

ryanabo commented 9 years ago

No problem, thanks for closing.

On Fri, Oct 2, 2015 at 4:08 PM, Jeff S Jasper notifications@github.com wrote:

Its been awhile but just noticed this was left open. The fix worked as expected. Thanks!!

— Reply to this email directly or view it on GitHub https://github.com/a-bioinformatician/BreaKmer/issues/9#issuecomment-145142638 .