From b15270081fc2b70d7b8c985ffe3ba3df8550886c Mon Sep 17 00:00:00 2001
From: Jaeyoung Chun <jaeyoung.chun@gmail.com>
Date: Tue, 13 Jul 2021 08:38:39 -0400
Subject: [PATCH] Add Cromwell version

---
 Dockerfile.cromwell     | 22 ++++++++++++++++++++++
 package-for-cromwell.sh | 36 ++++++++++++++++++++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 Dockerfile.cromwell
 create mode 100755 package-for-cromwell.sh

diff --git a/Dockerfile.cromwell b/Dockerfile.cromwell
new file mode 100644
index 0000000..d96a923
--- /dev/null
+++ b/Dockerfile.cromwell
@@ -0,0 +1,22 @@
+FROM centos:7
+
+LABEL maintainer="Jaeyoung Chun (chunj@mskcc.org)"
+
+ENV CELLRANGER_ARC_VERSION 1.0.1
+
+ENV PATH /opt/cellranger-arc-${CELLRANGER_ARC_VERSION}:$PATH
+
+RUN yum update -y && yum groups install "Development Tools" -y \
+    && yum install -y which
+
+# https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/downloads/1.0
+# cell ranger arc binaries
+RUN curl -o cellranger-arc-1.0.1.tar.gz "https://cf.10xgenomics.com/releases/cell-arc/cellranger-arc-1.0.1.tar.gz?Expires=1626187084&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1hcmMvY2VsbHJhbmdlci1hcmMtMS4wLjEudGFyLmd6IiwiQ29uZGl0aW9uIjp7IkRhdGVMZXNzVGhhbiI6eyJBV1M6RXBvY2hUaW1lIjoxNjI2MTg3MDg0fX19XX0_&Signature=OtILJaLKQ5dF3bbB9Scwpspv3yB0yUxpofMwnOqi1IJjXBa8WU56TXJhdhZSLY2sR0bx7~Oc4~6R2wBG0lvrmCho322-OOPQkzfFYcvUtrOMcN8TLt3IKTD868h6CySrf4BSBFvCL~-66Fb0ztMB3Z5EuwGcRBDRzvnxQH8aM8oh7GjyLll~AfeJMISwWUEWfoHMcXBQASSkWP4qp609zzmirecDKEtjuvZYp5HbJvOFObEDqi9Cabpz8A5VEenop0aEuv~OOCb3qk4bh1hqaN4nx6kfcZLHav83aJm4JVo3C39SAU-cl9YGn4ow-T8vW7wfiaAbX3swBk5QB~Qjaw__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA" \
+    && tar xzf cellranger-arc-${CELLRANGER_ARC_VERSION}.tar.gz \
+    && rm -rf cellranger-arc-${CELLRANGER_ARC_VERSION}.tar.gz \
+    && mv cellranger-arc-${CELLRANGER_ARC_VERSION} /opt/
+
+WORKDIR /opt
+
+# ENTRYPOINT [ "cellranger-arc" ]
+# CMD [ "--help"]
diff --git a/package-for-cromwell.sh b/package-for-cromwell.sh
new file mode 100755
index 0000000..2902862
--- /dev/null
+++ b/package-for-cromwell.sh
@@ -0,0 +1,36 @@
+#!/bin/bash
+
+source config.sh
+
+image_name="cromwell-${image_name}"
+
+echo "Building ${image_name}:${version}..."
+
+# hack: comment the ENTRYPOINT and CMD lines
+# https://github.com/broadinstitute/cromwell/issues/2461
+cat Dockerfile \
+    | sed 's/^ENTRYPOINT \[/# ENTRYPOINT \[/g' \
+    | sed 's/^CMD \[/# CMD \[/g' > Dockerfile.cromwell
+
+cat Dockerfile.cromwell
+
+# build it
+docker build -t ${image_name}:${version} -f Dockerfile.cromwell .
+
+echo "Packaging ${registry}/${image_name}:${version}..."
+
+#
+# tag it and push it to docker hub
+#
+
+docker tag ${image_name}:${version} ${registry}/${image_name}:${version}
+if [ $create_ecr_repo == 1 ]
+then
+    # only create if not exist
+    aws ecr describe-repositories --repository-name ${image_name} 2> /dev/null
+    if [ $? != 0 ]
+    then
+        aws ecr create-repository --repository-name ${image_name}
+    fi
+fi
+docker push ${registry}/${image_name}:${version}