From 593b7f222ccfeb04c412738f264af114adea1bc2 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 15 Nov 2021 12:21:34 -0600
Subject: [PATCH] Add combined Julia and bam-readcounts Dockerfile

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 julia_bam-readcounts/Dockerfile | 77 +++++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 julia_bam-readcounts/Dockerfile

diff --git a/julia_bam-readcounts/Dockerfile b/julia_bam-readcounts/Dockerfile
new file mode 100644
index 0000000..2a87a13
--- /dev/null
+++ b/julia_bam-readcounts/Dockerfile
@@ -0,0 +1,77 @@
+FROM mgibio/bam-readcount:1.0.0
+
+
+## Copied from https://github.com/docker-library/julia/blob/master/1.6/buster/Dockerfile
+RUN set -eux; \
+	apt-get update; \
+	apt-get install -y --no-install-recommends \
+		ca-certificates \
+# ERROR: no download agent available; install curl, wget, or fetch
+		curl \
+	; \
+	rm -rf /var/lib/apt/lists/*
+
+ENV JULIA_PATH /usr/local/julia
+ENV PATH $JULIA_PATH/bin:$PATH
+
+# https://julialang.org/juliareleases.asc
+# Julia (Binary signing key) <buildbot@julialang.org>
+ENV JULIA_GPG 3673DF529D9049477F76B37566E3C7DC03D6E495
+
+# https://julialang.org/downloads/
+ENV JULIA_VERSION 1.6.3
+
+RUN set -eux; \
+	\
+	savedAptMark="$(apt-mark showmanual)"; \
+	if ! command -v gpg > /dev/null; then \
+		apt-get update; \
+		apt-get install -y --no-install-recommends \
+			gnupg \
+			dirmngr \
+		; \
+		rm -rf /var/lib/apt/lists/*; \
+	fi; \
+	\
+# https://julialang.org/downloads/#julia-command-line-version
+# https://julialang-s3.julialang.org/bin/checksums/julia-1.6.3.sha256
+# this "case" statement is generated via "update.sh"
+	dpkgArch="$(dpkg --print-architecture)"; \
+	case "${dpkgArch##*-}" in \
+# amd64
+		amd64) tarArch='x86_64'; dirArch='x64'; sha256='c7459c334cd7c3e4a297baf52535937c6bad640e60882f9201a73bab9394314b' ;; \
+# arm32v7
+		armhf) tarArch='armv7l'; dirArch='armv7l'; sha256='7cf08affbad206bd3c1ef8bc117bf0aa6ac95d1666bf4c06f9d530cff29b2067' ;; \
+# arm64v8
+		arm64) tarArch='aarch64'; dirArch='aarch64'; sha256='df1a7e96f83b60fda54fd14713a373e37ac2d80fd11dbd708a77c8a22ab86e25' ;; \
+# i386
+		i386) tarArch='i686'; dirArch='x86'; sha256='06e3d64813e4ba6019d8d79e918c48af4943700bd1eb689c481d82a64f8c280a' ;; \
+# ppc64le
+		ppc64el) tarArch='ppc64le'; dirArch='ppc64le'; sha256='a3cb6f58ee93bbd3bd72ecd45b9f37bf5e16e9c0ef30ba17c809ec7cbb84ee96' ;; \
+		*) echo >&2 "error: current architecture ($dpkgArch) does not have a corresponding Julia binary release"; exit 1 ;; \
+	esac; \
+	\
+	folder="$(echo "$JULIA_VERSION" | cut -d. -f1-2)"; \
+	curl -fL -o julia.tar.gz.asc "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz.asc"; \
+	curl -fL -o julia.tar.gz     "https://julialang-s3.julialang.org/bin/linux/${dirArch}/${folder}/julia-${JULIA_VERSION}-linux-${tarArch}.tar.gz"; \
+	\
+	echo "${sha256} *julia.tar.gz" | sha256sum -c -; \
+	\
+	export GNUPGHOME="$(mktemp -d)"; \
+	gpg --batch --keyserver keyserver.ubuntu.com --recv-keys "$JULIA_GPG"; \
+	gpg --batch --verify julia.tar.gz.asc julia.tar.gz; \
+	command -v gpgconf > /dev/null && gpgconf --kill all; \
+	rm -rf "$GNUPGHOME" julia.tar.gz.asc; \
+	\
+	mkdir "$JULIA_PATH"; \
+	tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1; \
+	rm julia.tar.gz; \
+	\
+	apt-mark auto '.*' > /dev/null; \
+	[ -z "$savedAptMark" ] || apt-mark manual $savedAptMark; \
+	apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false; \
+	\
+# smoke test
+	julia --version
+
+CMD ["julia"]