README.md

In yasmina-mekki/gwhap: Genome wide haplotype analysis

gwhap

gwhap, the Genome-Wide HAPlotype analysis package

The gwhap software is related to the following paper : https://www.nature.com/articles/s41431-021-00827-8

Installation with a singularity container DURING development cycles

1. get a singularity that has devetools and IRkernels.
2. get a clone of the gwhap gitlab project
3. organize your directories to reflect the following envir varaibles (where is singularity and in which dir is gwhap.):

SINGU=/home/USERNAME/volatile/singularity/brainomics-ubuntu.simg
MY_HOME=/home/USERNAME/volatile/PROJECT

Then run :

singularity shell --home $MY_HOME:/home/jovyan $SINGU

From within the singularity

export R_LIBS=~/R

Then launch R

setwd("gwhap")
# this has to be replayed EACH time you modify the code
###############################
detach("package:gwhap", unload=TRUE)

devtools::document(roclets=c('rd', 'collate', 'namespace'))
devtools::build_vignettes()
devtools::build()


install.packages("../gwhap_0.2.tar.gz", repos=NULL)
library(gwhap)

###############################
# now run an exmaple
toy_to_run = system.file("example", "toy.R",package="gwhap")
source(toy_to_run)

or

R -e "setwd(\"gwhap\");devtools::document(roclets=c('rd', 'collate', 'namespace'))"
R CMD build --no-build-vignettes gwhap ; R CMD INSTALL gwhap_0.2.tar.gz

Installation

If run from within a singularity container:

export R_LIBS=<PAHTH into the container>/R

install.packages("gwhap.xxx.tar.gz",repos=NULL)

Documentation

package documentation is available after installation: (might need to reload R/rstudio session) ```{r package documentation, echo=TRUE} package?gwhap

or once it is loaded :
```{r package documentation 2, echo=TRUE}
library(gwhap)
?gwhap 

description and full documentation : ```{r package full documentation, echo=TRUE} library(help="gwhap")

```

yasmina-mekki/gwhap documentation built on Dec. 31, 2021, 9:19 p.m.