Set tmp file path

[mmoisse]

Is there a way to set the temp filepath?

I'm working on a cluster where I have a quota of 8GiB in my homedir. When I run multiple instances of CollapsABEL they all crash due to I/O error. I noticed that this is due to the fact that CollapsABEL makes temp files in in ${HOME}/.collapsabel/
I solved this by making ${HOME}/.collapsabel a symlink to a place without space quota. But it would be nice it this would a setting somewhere.

[kindlychung]

Yes, like this:

library(CollapsABEL)
collenv$.collapsabel_dir = "/tmp/collapsabel"
rbed_info = rbedInfo(bedstem = "test", TRUE)
pl_gwas = plGwas(rbed_info,
pheno = "test.phe",
pheno_name = "y",
covar_name = "sex,age",
gwas_tag = "test_y_sex_age")
gcdh_res = runGcdh(pl_gwas, n_shift = 5)

[kindlychung]

I forgot something, there are two other variables that can also be changed:

collenv$.collapsabel_dir = "/tmp/colldir"
collenv$.collapsabel_gwas = file.path(collenv$.collapsabel_dir, "gwas")
collenv$.collapsabel_gcdh = file.path(collenv$.collapsabel_dir, "gcdh")