Merge pull request #621 from MaxUlysse/Tests

Simplify tests

.travis.yml

@@ -1,40 +1,38 @@
 sudo: required
-
 language: java
-
 jdk: openjdk8
-
-services:
-  - docker
+services: docker
 
 addons:
   apt:
     update: true
 
 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"

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`

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