From a11cb5e7c357174c2ec8d4355b50f6d1bd0cce80 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Nov 2023 18:36:05 -0500
Subject: [PATCH 1/5] feat: create docker for ChIPseeker processes

---
 common/ccbr_chipseeker/Dockerfile      | 25 +++++++++++++++++++++++++
 common/ccbr_chipseeker/environment.txt | 17 +++++++++++++++++
 2 files changed, 42 insertions(+)
 create mode 100644 common/ccbr_chipseeker/Dockerfile
 create mode 100644 common/ccbr_chipseeker/environment.txt

diff --git a/common/ccbr_chipseeker/Dockerfile b/common/ccbr_chipseeker/Dockerfile
new file mode 100644
index 0000000..bda66c6
--- /dev/null
+++ b/common/ccbr_chipseeker/Dockerfile
@@ -0,0 +1,25 @@
+FROM nciccbr/ccbr_ubuntu_base_20.04:v6.1
+
+# build time variables
+ARG BUILD_DATE="000000"
+ENV BUILD_DATE=${BUILD_DATE}
+ARG BUILD_TAG="000000"
+ENV BUILD_TAG=${BUILD_TAG}
+ARG REPONAME="000000"
+ENV REPONAME=${REPONAME}
+
+# install R packages with conda
+COPY environment.txt /data2/
+RUN mamba install -c bioconda -c conda-forge --file /data2/environment.txt
+ENV R_LIBS_USER=/opt2/conda/lib/R/library/
+
+# cleanup etc
+# Save Dockerfile in the docker
+COPY Dockerfile /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+RUN chmod a+r /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+ENV PATH="/opt2/:$PATH"
+RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    apt-get autoclean && \
+    apt-get autoremove -y && \
+    rm -rf /var/lib/{apt,dpkg,cache,log}/
+WORKDIR /data2
\ No newline at end of file
diff --git a/common/ccbr_chipseeker/environment.txt b/common/ccbr_chipseeker/environment.txt
new file mode 100644
index 0000000..46e05d3
--- /dev/null
+++ b/common/ccbr_chipseeker/environment.txt
@@ -0,0 +1,17 @@
+r-base=4.3.1
+r-argparse
+r-BiocManager
+r-dplyr
+r-ggplot2
+r-glue
+bioconductor-ChIPseeker
+bioconductor-org.Bt.eg.db
+bioconductor-org.Hs.eg.db
+bioconductor-org.Mm.eg.db 
+bioconductor-org.Mmu.eg.db 
+bioconductor-TxDb.Btaurus.UCSC.bosTau9.refGene 
+bioconductor-TxDb.Hsapiens.UCSC.hg19.knownGene
+bioconductor-TxDb.Hsapiens.UCSC.hg38.knownGene
+bioconductor-TxDb.Mmulatta.UCSC.rheMac10.refGene
+bioconductor-bioconductor-TxDb.Mmusculus.UCSC.mm9.knownGene
+bioconductor-TxDb.Mmusculus.UCSC.mm10.knownGene
\ No newline at end of file

From c4328568764ca0509e53b08fddb3a64fb826bf79 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Nov 2023 18:41:28 -0500
Subject: [PATCH 2/5] fix: typo in pkg name

---
 common/ccbr_chipseeker/environment.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/common/ccbr_chipseeker/environment.txt b/common/ccbr_chipseeker/environment.txt
index 46e05d3..ecac0a6 100644
--- a/common/ccbr_chipseeker/environment.txt
+++ b/common/ccbr_chipseeker/environment.txt
@@ -13,5 +13,5 @@ bioconductor-TxDb.Btaurus.UCSC.bosTau9.refGene
 bioconductor-TxDb.Hsapiens.UCSC.hg19.knownGene
 bioconductor-TxDb.Hsapiens.UCSC.hg38.knownGene
 bioconductor-TxDb.Mmulatta.UCSC.rheMac10.refGene
-bioconductor-bioconductor-TxDb.Mmusculus.UCSC.mm9.knownGene
+bioconductor-TxDb.Mmusculus.UCSC.mm9.knownGene
 bioconductor-TxDb.Mmusculus.UCSC.mm10.knownGene
\ No newline at end of file

From 2b84b8e4828044284bd377d7861c3df2733b2680 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Nov 2023 19:40:52 -0500
Subject: [PATCH 3/5] fix: uninstall R from base image

---
 common/ccbr_chipseeker/Dockerfile | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/common/ccbr_chipseeker/Dockerfile b/common/ccbr_chipseeker/Dockerfile
index bda66c6..a630494 100644
--- a/common/ccbr_chipseeker/Dockerfile
+++ b/common/ccbr_chipseeker/Dockerfile
@@ -8,6 +8,11 @@ ENV BUILD_TAG=${BUILD_TAG}
 ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
+# uninstall R from base image
+RUN apt-get --purge remove r-base r-base-dev r-recommended r-cran-* && \
+    apt-get autoremove && \
+    apt-get update
+
 # install R packages with conda
 COPY environment.txt /data2/
 RUN mamba install -c bioconda -c conda-forge --file /data2/environment.txt

From c3becd3c14dcfe79e9f05ac6f4662b830e04d505 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Nov 2023 20:03:35 -0500
Subject: [PATCH 4/5] fix: frontend is noninteractive

---
 common/ccbr_chipseeker/Dockerfile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/common/ccbr_chipseeker/Dockerfile b/common/ccbr_chipseeker/Dockerfile
index a630494..238ffbc 100644
--- a/common/ccbr_chipseeker/Dockerfile
+++ b/common/ccbr_chipseeker/Dockerfile
@@ -9,7 +9,8 @@ ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
 # uninstall R from base image
-RUN apt-get --purge remove r-base r-base-dev r-recommended r-cran-* && \
+RUN DEBIAN_FRONTEND=noninteractive apt-get --purge remove \
+    r-base r-base-dev r-recommended r-cran-* && \
     apt-get autoremove && \
     apt-get update
 

From 29a00dcb3c9515ba0e616e8c8532466c0f21cbe2 Mon Sep 17 00:00:00 2001
From: Kelly Sovacool <kelly.sovacool@nih.gov>
Date: Wed, 15 Nov 2023 20:12:12 -0500
Subject: [PATCH 5/5] fix: use newer base image which doesn't have R installed

---
 common/ccbr_chipseeker/Dockerfile | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/common/ccbr_chipseeker/Dockerfile b/common/ccbr_chipseeker/Dockerfile
index 238ffbc..bda66c6 100644
--- a/common/ccbr_chipseeker/Dockerfile
+++ b/common/ccbr_chipseeker/Dockerfile
@@ -8,12 +8,6 @@ ENV BUILD_TAG=${BUILD_TAG}
 ARG REPONAME="000000"
 ENV REPONAME=${REPONAME}
 
-# uninstall R from base image
-RUN DEBIAN_FRONTEND=noninteractive apt-get --purge remove \
-    r-base r-base-dev r-recommended r-cran-* && \
-    apt-get autoremove && \
-    apt-get update
-
 # install R packages with conda
 COPY environment.txt /data2/
 RUN mamba install -c bioconda -c conda-forge --file /data2/environment.txt