fixing 02 apptainer

MRCIEU · Jan 16, 2025 · 9a0673f · 9a0673f
1 parent 3d646c5
commit 9a0673f
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -43,4 +43,5 @@ RUN R -e 'options( \
     renv::install(c("stringi", "git2r")); \
     renv::restore(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest"))'
 
-COPY . .
+COPY . .
+COPY .git/ ./.git/
diff --git a/resources/phenotypes/organise_phenotypes.rmd b/resources/phenotypes/organise_phenotypes.rmd
@@ -149,8 +149,7 @@ organise_phenotype("bmiz", phenotypes, df, gen_covs, covdat, agebins, pl=TRUE)
 Get git version
 
 ```{r version}
-g <- git2r::revparse_single(here(), "HEAD")
-g
+try(git2r::revparse_single(here(), "HEAD"), silent=TRUE)
 ```
 
 Session info

diff --git a/resources/render.r b/resources/render.r
@@ -2,4 +2,5 @@ library(here)
 library(rmarkdown)
 
 args <- commandArgs(T)
-rmarkdown::render(args[1], output_dir=args[2])
+print(args)
+rmarkdown::render(args[1], intermediates_dir=args[2], knit_root_dir=args[2], output_dir=args[2])