From c2e37a5e80d08365fcd6d6c8d26b407489c60def Mon Sep 17 00:00:00 2001
From: jharenza <jharenza@gmail.com>
Date: Thu, 2 May 2024 20:04:05 +0000
Subject: [PATCH 1/3] update dockerfile R 4.4, BioC 3.19

---
 Dockerfile | 60 ++++++++++++++++++++++++++----------------------------
 1 file changed, 29 insertions(+), 31 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 29eaf836..1d845883 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,12 +1,8 @@
-FROM rocker/tidyverse:4.2
+FROM rocker/tidyverse:4.4.0
 
 LABEL maintainer = "Ryan Corbett (corbettr@chop.edu)"
 
-COPY scripts/install_github.r .
 
-COPY scripts/install_bioc.r .
-
-### Install apt-getable packages to start
 #########################################
 RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
 
@@ -25,34 +21,36 @@ RUN apt-get -y --no-install-recommends install \
     libudunits2-dev \
     libmagick++-dev
 
-# install R packages from CRAN
-RUN install2.r \
-	BiocManager \
-	circlize \
-  data.table \
-  ggalluvial \
-  ggpubr \
-  ggthemes \
-	optparse \
-	pheatmap \
-	RColorBrewer \
-	survival \
-  survMisc \
-  survminer \
-  tidytext \
-  openxlsx \
-  
-  # install R packages from Bioconductor 
-RUN ./install_bioc.r \
-  biomaRt \
-  ComplexHeatmap \
-  GenomicRanges
+# Set the Bioconductor repository as the primary repository
+RUN R -e "options(repos = BiocManager::repositories())"
+
+# Install BiocManager and the desired version of Bioconductor
+RUN R -e "install.packages('BiocManager', dependencies=TRUE)"
+RUN R -e "BiocManager::install(version = '3.19')"
+
+# Install packages
+RUN R -e 'BiocManager::install(c( \
+  "biomaRt", \
+  "circlize", \
+  "ComplexHeatmap", \
+  "data.table", \
+  "GenomicRanges", \
+  "ggalluvial", \
+  "ggthemes", \
+  "optparse", \
+  "pheatmap", \
+  "RColorBrewer", \
+  "survival", \
+  "survMisc", \
+  "survminer", \
+  "tidytext", \
+  "openxlsx" \
+))'
   
-RUN ./install_github.r \
-	clauswilke/colorblindr
 	
-RUN ./install_github.r  'thomasp85/patchwork' --ref 'c67c6603ba59dd46899f17197f9858bc5672e9f4'
+RUN R -e "remotes::install_github('clauswilke/colorblindr', ref = '1ac3d4d62dad047b68bb66c06cee927a4517d678', dependencies = TRUE)"
+RUN R -e "remotes::install_github('thomasp85/patchwork', ref = 'c67c6603ba59dd46899f17197f9858bc5672e9f4')"
 	
 WORKDIR /rocker-build/
 
-ADD Dockerfile . 
\ No newline at end of file
+ADD Dockerfile . 

From d5afa591ff9c48d3af8c1b510471154eaa78c3b7 Mon Sep 17 00:00:00 2001
From: jharenza <jharenza@gmail.com>
Date: Thu, 2 May 2024 20:54:32 +0000
Subject: [PATCH 2/3] update to patchwork 1.2.0

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 1d845883..955f0b8a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -49,7 +49,7 @@ RUN R -e 'BiocManager::install(c( \
   
 	
 RUN R -e "remotes::install_github('clauswilke/colorblindr', ref = '1ac3d4d62dad047b68bb66c06cee927a4517d678', dependencies = TRUE)"
-RUN R -e "remotes::install_github('thomasp85/patchwork', ref = 'c67c6603ba59dd46899f17197f9858bc5672e9f4')"
+RUN R -e "remotes::install_github('thomasp85/patchwork', ref = '1cb732b129ed6a65774796dc1f618558c7498b66')"
 	
 WORKDIR /rocker-build/
 

From 0e0518cedfd4e78c3203d619fcf80152609fd100 Mon Sep 17 00:00:00 2001
From: Jo Lynne Rokita <jharenza@gmail.com>
Date: Thu, 2 May 2024 18:02:32 -0400
Subject: [PATCH 3/3] move github action out, update readme

---
 .../{workflows => }/continuous_integration.yml   |   0
 .github/workflows/.DS_Store                      | Bin 0 -> 6148 bytes
 README.md                                        |  11 +++++++----
 3 files changed, 7 insertions(+), 4 deletions(-)
 rename .github/{workflows => }/continuous_integration.yml (100%)
 create mode 100644 .github/workflows/.DS_Store

diff --git a/.github/workflows/continuous_integration.yml b/.github/continuous_integration.yml
similarity index 100%
rename from .github/workflows/continuous_integration.yml
rename to .github/continuous_integration.yml
diff --git a/.github/workflows/.DS_Store b/.github/workflows/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
GIT binary patch
literal 6148
zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3
zem<@ulZcFPQ@L2!n>{z**<q8>++&mCkOWA81W14cNZ<zv;LbK1Poaz?KmsK2CSc!(
z0ynLxE!0092;Krf2c+FF_Fe*7ECH>lEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ
zLs35+`xjp>T0<F0fCPF1$Cyrb|F7^5{eNG?83~ZUUlGt@xh*qZDeu<Z%US-OSsOPv
j)R!Z4KLME7ReXlK;d!wEw5GODWMKRea10D2@KpjYNUI8I

literal 0
HcmV?d00001

diff --git a/README.md b/README.md
index 5c22de4b..e2abe8c6 100644
--- a/README.md
+++ b/README.md
@@ -4,17 +4,20 @@
 
 1. Clone the repository:
 ```
-    git clone https://github.com/d3b-center/pbta-ancestry.git
+git clone git@github.com:d3b-center/pbta-ancestry.git
 ```
+
 2. Pull Docker container:
 ```
-    docker pull pgc-images.sbgenomics.com/corbettr/pbta-ancestry:latest
+docker pull pgc-images.sbgenomics.com/d3b-bixu/pbta-ancestry:latest
 ```
+
 3. Start the Docker container; from the `pbta-ancestry` folder, run:
 ```
-    docker run --platform linux/amd64 --name <CONTAINER_NAME> -d -e PASSWORD=pass -p 8787:8787 -v $PWD:/home/rstudio/pbta-ancestry pgc-images.sbgenomics.com/corbettr/pbta-ancestry:latest
+docker run --platform linux/amd64 --name <CONTAINER_NAME> -d -e PASSWORD=pass -p 8787:8787 -v $PWD:/home/rstudio/pbta-ancestry pgc-images.sbgenomics.com/d3b-bixu/pbta-ancestry:latest
 ```
+
 4. Execute the shell within the docker image; from the `pbta-ancestry` folder, run: 
 ```
-    docker exec -ti <CONTAINER_NAME> bash
+docker exec -ti <CONTAINER_NAME> bash
 ```
\ No newline at end of file