From 4bb709c04d56a6f7f3834eaa5bf6b31131ae9013 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 16 Aug 2018 16:38:44 +0200 Subject: [PATCH 1/3] simpler tests --- .travis.yml | 56 ++++++++++++++++++++++++++--------------------------- 1 file changed, 27 insertions(+), 29 deletions(-) diff --git a/.travis.yml b/.travis.yml index 1aab116101..3e18eb1d1d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,11 +1,7 @@ sudo: required - language: java - jdk: openjdk8 - -services: - - docker +services: docker addons: apt: @@ -13,28 +9,30 @@ addons: env: global: - - NXF_VER=0.31.0 SGT_VER=2.4.2 + - NXF_VER=0.31.0 SGT_VER=2.5.1 matrix: - - PROFILE=singularity TEST=TOOLS TOOL_INSTALL=all - - PROFILE=singularity TEST=MANTA TOOL_INSTALL=all - - PROFILE=docker TEST=MANTA TOOL_INSTALL=nextflow - - PROFILE=docker TEST=TOOLS TOOL_INSTALL=nextflow - - PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow - - PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all - - PROFILE=singularity TEST=STEP TOOL_INSTALL=all - - PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all - - PROFILE=singularity TEST=DIR TOOL_INSTALL=all - - PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow - - PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow - - PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow - - PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow - -install: # Install Nextflow (and Singularity if needed) - - "./scripts/install.sh --tool $TOOL_INSTALL" - - "travis_retry ./scripts/containers.sh --profile $PROFILE --test $TEST" - -before_script: # Build references when needed - - "./scripts/test.sh --profile $PROFILE --test $TEST --build" - -script: - - "./scripts/test.sh --profile $PROFILE --test $TEST" + - CE=singularity TEST=TOOLS + - CE=singularity TEST=MANTA + - CE=docker TEST=MANTA + - CE=docker TEST=TOOLS + - CE=docker TEST=ANNOTATEVEP + - CE=singularity TEST=ANNOTATESNPEFF + - CE=singularity TEST=STEP + - CE=singularity TEST=GERMLINE + - CE=singularity TEST=DIR + - CE=docker TEST=ANNOTATESNPEFF + - CE=docker TEST=STEP + - CE=docker TEST=GERMLINE + - CE=docker TEST=DIR + +install: + # Install Nextflow (and Singularity if needed) + - "./scripts/install.sh --engine $CE" + # Donwload big containers for ANNOTATEVEP and ANNOTATESNPEF tests) + - "travis_retry ./scripts/containers.sh --profile $CE --test $TEST" + +# Build references when needed +before_script: "./scripts/test.sh --profile $CE --test $TEST --build" + +# Actual tests +script: "./scripts/test.sh --profile $CE --test $TEST" From 54cf6a7414753791db9889d4c60e29fd74d6d0c9 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 16 Aug 2018 16:39:59 +0200 Subject: [PATCH 2/3] improve install script --- scripts/install.sh | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/scripts/install.sh b/scripts/install.sh index 66e1daa1c7..cd466415dd 100755 --- a/scripts/install.sh +++ b/scripts/install.sh @@ -1,14 +1,14 @@ #!/bin/bash set -euo pipefail -TOOL="all" +CONTAINER_ENGINE="singularity" while [[ $# -gt 0 ]] do key="$1" case $key in - -t|--tool) - TOOL="$2" + -e|--engine) + CONTAINER_ENGINE="$2" shift # past argument shift # past value ;; @@ -19,25 +19,27 @@ do done # Install Nextflow -if [[ "$TOOL" = nextflow ]] || [[ "$TOOL" = all ]] -then - cd $HOME - curl -fsSL get.nextflow.io | bash - chmod +x nextflow - sudo mv nextflow /usr/local/bin/ -fi +mkdir /tmp/nextflow +cd /tmp/nextflow +wget -qO- get.nextflow.io | bash +sudo ln -s /tmp/nextflow/nextflow /usr/local/bin/nextflow # Install Singularity -if [[ "$TOOL" = singularity ]] || [[ "$TOOL" = all ]] +if [[ "$CONTAINER_ENGINE" = singularity ]] then - sudo apt-get install squashfs-tools - cd $HOME + if [[ "$SGT_VER" = '' ]] + then + SGT_VER=$(curl --silent "https://api.github.com/repos/Singularityware/Singularity/releases/latest" | grep -Po '"tag_name": "\K.*?(?=")') + fi + sudo apt-get install libarchive-dev squashfs-tools + mkdir /tmp/singularity + cd /tmp/singularity wget https://github.com/singularityware/singularity/releases/download/$SGT_VER/singularity-$SGT_VER.tar.gz tar xvf singularity-$SGT_VER.tar.gz cd singularity-$SGT_VER ./configure --prefix=/usr/local make sudo make install - cd .. - rm -rf singularity-$SGT_VER* + cd ${TRAVIS_BUILD_DIR} + rm -rf /tmp/singularity fi From b07b9d1280fd59cde806d7eacb6f0cb4e9560741 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Fri, 17 Aug 2018 10:15:06 +0200 Subject: [PATCH 3/3] Update CHANGELOG --- CHANGELOG.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 20502ea188..b45791ca4e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,10 +16,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG - [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines` +- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Improve install script +- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Simplify tests ### `Removed` - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template +### `Fixed` +- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Fix VEP tests + ## [2.1.0] - Ruotes - 2018-08-14 ### `Added`