From 962ac77e49b5e9bafdf56e678b677f0b705b1482 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Fri, 29 Jan 2021 11:28:25 +0100
Subject: [PATCH] docker: add samtools v1.11
---
src/.docker_modules/samtools/1.11/Dockerfile | 27 +++++++++++++++++++
.../samtools/1.11/docker_init.sh | 4 +++
src/nf_modules/samtools/main.nf | 2 +-
3 files changed, 32 insertions(+), 1 deletion(-)
create mode 100644 src/.docker_modules/samtools/1.11/Dockerfile
create mode 100755 src/.docker_modules/samtools/1.11/docker_init.sh
diff --git a/src/.docker_modules/samtools/1.11/Dockerfile b/src/.docker_modules/samtools/1.11/Dockerfile
new file mode 100644
index 00000000..054c3e6e
--- /dev/null
+++ b/src/.docker_modules/samtools/1.11/Dockerfile
@@ -0,0 +1,27 @@
+FROM alpine:3.8
+MAINTAINER Laurent Modolo
+
+ENV SAMTOOLS_VERSION=1.11
+ENV PACKAGES git \
+ make \
+ gcc \
+ musl-dev \
+ zlib-dev \
+ ncurses-dev \
+ bzip2-dev \
+ xz-dev \
+ curl-dev \
+ bash
+
+RUN apk update && \
+ apk add ${PACKAGES}
+
+RUN git clone https://github.com/samtools/htslib.git && \
+cd htslib && \
+git checkout ${SAMTOOLS_VERSION} && \
+cd .. && \
+git clone https://github.com/samtools/samtools.git && \
+cd samtools && \
+git checkout ${SAMTOOLS_VERSION} && \
+make && \
+cp samtools /usr/bin/
diff --git a/src/.docker_modules/samtools/1.11/docker_init.sh b/src/.docker_modules/samtools/1.11/docker_init.sh
new file mode 100755
index 00000000..e5cf9c28
--- /dev/null
+++ b/src/.docker_modules/samtools/1.11/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull lbmc/samtools:1.11
+docker build src/.docker_modules/samtools/1.11 -t 'lbmc/samtools:1.11'
+docker push lbmc/samtools:1.11
diff --git a/src/nf_modules/samtools/main.nf b/src/nf_modules/samtools/main.nf
index 3b0c8f34..1f5cc1b6 100644
--- a/src/nf_modules/samtools/main.nf
+++ b/src/nf_modules/samtools/main.nf
@@ -1,4 +1,4 @@
-version = "1.7"
+version = "1.11"
container_url = "lbmc/samtools:${version}"
process filter_bam {
--
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