diff --git a/src/docker_modules/picard/2.18.11/Dockerfile b/src/docker_modules/picard/2.18.11/Dockerfile new file mode 100644 index 0000000000000000000000000000000000000000..6a358e55bf36a4be4842335f47491ec8ac3a4ced --- /dev/null +++ b/src/docker_modules/picard/2.18.11/Dockerfile @@ -0,0 +1,19 @@ +FROM ubuntu:18.04 +MAINTAINER Laurent Modolo + +ENV PICARD_VERSION=2.18.11 +ENV PACKAGES default-jre=2:1.1* \ + curl=7.58.0* \ + ca-certificates=20180409 + + +RUN apt-get update && \ + apt-get install -y --no-install-recommends ${PACKAGES} && \ + apt-get clean + +RUN curl -k -L https://github.com/broadinstitute/picard/releases/download/${PICARD_VERSION}/picard.jar -o picard.jar && \ + mkdir -p /usr/share/java/ && \ + mv picard.jar /usr/share/java/ + +COPY PicardCommandLine /usr/bin/ +RUN chmod +x /usr/bin/PicardCommandLine diff --git a/src/docker_modules/picard/2.18.11/PicardCommandLine b/src/docker_modules/picard/2.18.11/PicardCommandLine new file mode 100644 index 0000000000000000000000000000000000000000..ce067365785f2f03c722668eff8d80a94b9b34d3 --- /dev/null +++ b/src/docker_modules/picard/2.18.11/PicardCommandLine @@ -0,0 +1,15 @@ +#!/bin/sh +set -eu +PRG="$(basename -- "$0")" +case "$PRG" in +picard-tools) + echo 1>&2 'Warning: picard-tools is deprecated and should be replaced by PicardCommandLine' + ;; +PicardCommandLine) + ;; +*) + set -- "$PRG" "$@" + ;; +esac + +exec java ${JAVA_OPTIONS-} -jar /usr/share/java/picard.jar "$@" diff --git a/src/docker_modules/picard/2.18.11/docker_init.sh b/src/docker_modules/picard/2.18.11/docker_init.sh new file mode 100755 index 0000000000000000000000000000000000000000..7546e343730c0380b749031baec984c1838b3a88 --- /dev/null +++ b/src/docker_modules/picard/2.18.11/docker_init.sh @@ -0,0 +1,2 @@ +#!/bin/sh +docker build src/docker_modules/picard/2.18.11 -t 'picard:2.18.11'