From 9a0673f4c5cd9f64467fd239065d14400047afc9 Mon Sep 17 00:00:00 2001
From: Gibran Hemani <explodecomputer@gmail.com>
Date: Thu, 16 Jan 2025 15:42:10 +0000
Subject: [PATCH] fixing 02 apptainer

---
 Dockerfile                                   | 3 ++-
 resources/phenotypes/organise_phenotypes.rmd | 3 +--
 resources/render.r                           | 3 ++-
 3 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 306138b..b56b581 100644
--- 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 . .
\ No newline at end of file
+COPY . .
+COPY .git/ ./.git/
diff --git a/resources/phenotypes/organise_phenotypes.rmd b/resources/phenotypes/organise_phenotypes.rmd
index dffdb97..544bf2d 100755
--- 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
index 512c4a9..e00dccb 100644
--- 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])
\ No newline at end of file