Commit 60f0c861 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.18.2+dfsg

parent 5b5cca4c

.dockerignore

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.git

.gitignore

.jar_opt

.classpath

.pullapprove.yml

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version: 2



group_defaults:

  approve_by_comment:

    approve_regex: '^:\+1:'

    enabled: true



groups:

  reviewers:

    required: 1

    conditions:

      branches:

        - master

    teams:

      - dsde-pipelines-developers

    users:

      - nh13

      - tfenne

      - yfarjoun

.travis.yml

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dist: trusty

language: java

before_cache:

  - rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
@@ -8,6 +9,7 @@ cache: 
    - $HOME/.m2

jdk:

  - oraclejdk8

  - openjdk8

before_install:

  - wget -q -O - https://dl.google.com/linux/linux_signing_key.pub | sudo apt-key add -

  - sudo apt-get -qq update
@@ -15,3 +17,6 @@ before_install: 
script: ./gradlew jacocoTestReport

after_success:

  - ./gradlew coveralls

  - if [ "$TRAVIS_BRANCH" == "master" ]; then

        ./gradlew uploadArchives;

    fi

Dockerfile

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@@ -10,23 +10,19 @@ RUN apt-get update && \ 
    apt-get autoremove -y



# Assumes Dockerfile lives in root of the git repo. Pull source files into container

COPY build.xml /usr/picard/build.xml

COPY src /usr/picard/src

COPY lib /usr/picard/lib

COPY / /usr/picard/

WORKDIR /usr/picard



# Clone out htsjdk. First turn off git ssl verification

RUN git config --global http.sslVerify false && git clone https://github.com/samtools/htsjdk.git



# Build the distribution jar, clean up everything else

RUN ant clean all && \

    mv dist/picard.jar picard.jar && \

    mv src/scripts/picard/docker_helper.sh docker_helper.sh && \

    ant clean && \

    rm -rf htsjdk && \

RUN ./gradlew shadowJar && \

    mv build/libs/picard.jar picard.jar && \

    mv src/main/resources/picard/docker_helper.sh docker_helper.sh && \

    ./gradlew clean && \

    rm -rf src && \

    rm -rf lib && \

    rm build.xml

    rm -rf gradle && \

    rm -rf .git && \

    rm gradlew && \

    rm build.gradle



RUN mkdir /usr/working

WORKDIR /usr/working

LICENSE.txt

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MIT License



Copyright (c) 2017 Broad Institute



Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in all

copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

SOFTWARE.