[maker-devel] Maker example data for 2013 GMOD summer school

[Carson Holt]

Use maker with MPI. MPI does not just have to be on a cluster, it can be installed on a local computer or server (you probably already have it installed and don’t realize it). Instructions on how to setup MAKER with MPI are in the README and INSTALL files in the download.

Example command (on a single machine 16 core server):
mpiexec -n <cpu_count> maker
mpiexec -n 16 maker

Run across multiple machines (ten 16 core servers):
mpiexec -hostfile <list_of_hosts> -n <cpu_count> maker
mpiexec  -hostfile ip_list -n 160 maker

The second option requires a network mounted working directory accessible to all machines.

—Carson



> On Apr 27, 2016, at 12:06 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Hi, Daniel
> 
> I am using Maker to annotate cowpea genome for a while but now I am wondering if I could use multi-threads instead of single one? It has been running tblastx for such a long time using single thread. But I couldn’t find such settings in documentations to assign multi-threads to run Maker. Is there such an option?
> 
> Thank you 
> Qihua
> 
> 
>> On Mar 30, 2016, at 2:17 PM, Daniel Ence <dence at genetics.utah.edu> wrote:
>> 
>> HI Qihua, 
>> 
>> I believe that most of the data we used in the tutorials are are available in the maker/data directory, which is included in all maker distributions. Please let me know if that isn’t the case. 
>> 
>> ~Daniel
>> 
>> 
>> Daniel Ence
>> Graduate Student
>> Eccles Institute of Human Genetics
>> University of Utah
>> 15 North 2030 East, Room 2100
>> Salt Lake City, UT 84112-5330
>> 
>>> On Mar 30, 2016, at 3:10 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
>>> 
>>> Hi Michael and Daniel,
>>> 
>>> I am a graduate student in UC Riverside, and recently I am learning to use Maker for genome annotation. I was trying to find some tutorials to follow and practice on example data, and I found out that you were giving a talk on Maker during 2013 GMOD summer school and the tutorial of that is very detailed. Nice job!
>>> 
>>> But example data under the folder you mentioned as ./maker/maker_course is not provided on the website and I am wondering if they are available to the public or not. If yes, could you send me those materials so that I could follow your tutorial to practice using Maker?
>>> 
>>> Thank you
>>> Best
>>> Qihua
>> 
> 
>