In pvrqualitasag/qgert: Qualitas Genetic Evaluation Routine Tools

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(qgert)

Usage

The split of the gsRuns can be done using the following shell script

```{bash, eval=FALSE} cd /qualstorzws01/data_zws/gs ./prog/split_gsRuns_sorted_rt.sh -g work/gsRuns.txt -d 1908 -m first -n 100

This uses the gsRuns-list stored under `work/gsRuns.txt`, it takes the runtime information from the logfiles of the archive of the 1908 evaluation and it produces 100 small job files.


## Update and Installation
This script can only be used if the R-package `qgert` is installed. On the ZWS-servers this is the case. An update of the package can be done with

```r
# install.packages("devtools")
devtools::install_github("pvrqualitasag/qgert")

Then the bash script split_gsRuns_sorted_rt.sh must be installed into the subdirectory prog of the GS-evaluation directory

{bash, eval=FALSE} /home/zws/lib/R/library/qgert/bash/install_script.sh -s ~/lib/R/library/qgert/bash/split_gsRuns_sorted_rt.sh -t /qualstorzws01/data_zws/gs/prog

Purpose - Why This Is Done

Estimation of marker effects and reliability prediction is a resource intensive step during the routine genetic evaluation. Hence all these estimation tasks must be parallelized. Given a list (gsRuns-list) of computation jobs which consist of combinations of breeds, evaluation type, trait and parameter type, this list is to be split into a number of smaller lists.

As an additional requirement, the produced number of lists should contain the jobs sorted according to their predicted running time from a previous evaluation.

Description - How This Is Done

Given a directory where the logfiles of the previous evaluation is archived (or just a simple run-label such as 1908), the logfiles are searched for the predicted running time of the respective estimation job. This information is written to an outputfile. The outputfile is read into R where the records are sorted according to their running times. After the sort, a specified number of job-files is written. These files have the name-prefix gsSortedRuns.txt followed by a number.

To prepare the binary version of the SNP-Data one gsRun-job per breed is written to the file gsRuns.txt.snpBin. The jobs that are contained in gsRuns.txt.snpBin are not contained in the gsSortedRuns.txt-files. Hence all the programs with partitioned gs-Runs-lists, gsRuns.txt.snpBin must also be used as an argument.

pvrqualitasag/qgert documentation built on June 29, 2021, 11:14 p.m.