From 5090e8a5b4363b34097da0c6f9022aae85cbfe16 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 6 Jan 2022 10:25:57 +0100
Subject: [PATCH] Docker: add samtools 1.14
---
src/.docker_modules/samtools/1.14/Dockerfile | 41 +++++++++++++++++++
.../samtools/1.14/docker_init.sh | 5 +++
2 files changed, 46 insertions(+)
create mode 100644 src/.docker_modules/samtools/1.14/Dockerfile
create mode 100755 src/.docker_modules/samtools/1.14/docker_init.sh
diff --git a/src/.docker_modules/samtools/1.14/Dockerfile b/src/.docker_modules/samtools/1.14/Dockerfile
new file mode 100644
index 00000000..0ea86627
--- /dev/null
+++ b/src/.docker_modules/samtools/1.14/Dockerfile
@@ -0,0 +1,41 @@
+FROM quay.io/biocontainers/samtools:1.14--hb421002_0 AS build
+
+# ldd /usr/local/bin/samtools
+# linux-vdso.so.1 (0x00007ffec91ca000)
+# libhts.so.3 => /usr/local/bin/../lib/libhts.so.3 (0x00007fa2fc31f000)
+# libtinfow.so.6 => /usr/local/bin/../lib/libtinfow.so.6 (0x00007fa2fc2e0000)
+# libncursesw.so.6 => /usr/local/bin/../lib/libncursesw.so.6 (0x00007fa2fc2a3000)
+# libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fa2fc11f000)
+# libz.so.1 => /usr/local/bin/../lib/libz.so.1 (0x00007fa2fc105000)
+# libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa2fc0e4000)
+# libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa2fbf21000)
+# libdeflate.so.0 => /usr/local/bin/../lib/./libdeflate.so.0 (0x00007fa2fbf11000)
+# liblzma.so.5 => /usr/local/bin/../lib/./liblzma.so.5 (0x00007fa2fbee8000)
+# libbz2.so.1.0 => /usr/local/bin/../lib/./libbz2.so.1.0 (0x00007fa2fbed4000)
+# libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa2fbecf000)
+# /lib64/ld-linux-x86-64.so.2 (0x00007fa2fc4af000)
+# librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fa2fbec3000)
+
+ENV SAMTOOLS_VERSION=1.14
+ENV PACKAGES bash
+FROM alpine:3.8 AS env
+RUN apk update && \
+ apk add ${PACKAGES}
+COPY --from=build \
+ /usr/local/bin/samtools /usr/local/bin/
+COPY --from=build \
+ /usr/local/bin/../lib/libhts.so.3 \
+ /usr/local/lib/libtinfow.so.6 \
+ /usr/local/lib/libncursesw.so.6 \
+ /usr/local/lib/libz.so.1 \
+ /usr/local/lib/libdeflate.so.0 \
+ /usr/local/lib/liblzma.so.5 \
+ /usr/local/lib/libbz2.so.1.0 /usr/local/lib/
+COPY --from=build \
+ /lib/x86_64-linux-gnu/libm.so.6 \
+ /lib/x86_64-linux-gnu/libpthread.so.0 \
+ /lib/x86_64-linux-gnu/libc.so.6 \
+ /lib/x86_64-linux-gnu/libdl.so.2 \
+ /lib/x86_64-linux-gnu/librt.so.1 /lib/x86_64-linux-gnu/
+COPY --from=build \
+ /lib64/ld-linux-x86-64.so.2 /lib64/
\ No newline at end of file
diff --git a/src/.docker_modules/samtools/1.14/docker_init.sh b/src/.docker_modules/samtools/1.14/docker_init.sh
new file mode 100755
index 00000000..1d4a215f
--- /dev/null
+++ b/src/.docker_modules/samtools/1.14/docker_init.sh
@@ -0,0 +1,5 @@
+#!/bin/sh
+docker pull lbmc/samtools:1.14
+# docker build src/.docker_modules/samtools/1.14 -t 'lbmc/samtools:1.14'
+# docker push lbmc/samtools:1.14
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/samtools:1.14" --push src/.docker_modules/samtools/1.14
--
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