ldjump
Link to section 'Introduction' of 'ldjump' Introduction
LDJump is an R package to estimate variable recombination rates from population genetic data.
Home page: https://github.com/PhHermann/LDJump
Link to section 'Versions' of 'ldjump' Versions
- 0.3.1
Link to section 'Commands' of 'ldjump' Commands
- R
- Rscript
Link to section 'Module' of 'ldjump' Module
You can load the modules by:
module load biocontainers
module load ldjump
A full path to the Phi file of PhiPack needs to be provided as follows pathPhi = "/opt/PhiPack/Phi". In order to use LDhat to quickly calculate some of the summary statistics, please set pathLDhat = "/opt/LDhat/".
Link to section 'Interactive job' of 'ldjump' Interactive job
To run interactively on our clusters:
(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers ldjump
(base) UserID@bell-a008:~ $ R
R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(LDJump)
> LDJump(seqFullPath, alpha = 0.05, segLength = 1000, pathLDhat = "/opt/LDhat/", pathPhi = "/opt/PhiPack/Phi", format = "fasta", refName = NULL,
start = NULL, constant = F, status = T, cores = 1, accept = F, demography = F, out = "")
Link to section 'Batch job' of 'ldjump' Batch job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run ldjump on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ldjump
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers ldjump
Rscript script.R