.travis.yml

os: linux
dist: xenial

language: "perl"

perl:
  - "5.28"
  - "5.26"
  - "5.24"

services:
  - mysql

env:
  - COVERALLS=false DB=mysql

addons:
    apt:
        packages:
        - unzip
        - graphviz

before_install:
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-variation.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-taxonomy.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-external.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-killlist.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-pipeline.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-compara.git
    - git clone --quiet --branch release/90 --depth 1 https://github.com/Ensembl/ensembl-funcgen.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-hive.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-io.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-test.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/ensembl-production.git
    - git clone --quiet --depth 1 https://github.com/Ensembl/GIFTS.git
    - echo "We need release 56 for FuncGen modules"
    - git clone --quiet --branch release/56 --depth 1 https://github.com/Ensembl/ensembl.git ensembl-56
    - git clone --quiet --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
    - git clone --quiet --branch release-1-6-9 --depth 1 https://github.com/bioperl/bioperl-run.git
#Installing dependencies for ensembl and ensembl-hive
    - cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
    - cpanm --quiet --installdeps --with-recommends --notest --cpanfile ensembl-hive/cpanfile .
# htslib
    - wget https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2
    - tar -jxvf htslib-1.3.2.tar.bz2
    - cd htslib-1.3.2 && make CFLAGS="-g -O2 -fPIC" && cd ..
# samtools
    - wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2
    - tar -jxvf samtools-1.15.1.tar.bz2
    - cd samtools-1.15.1 && ./configure --prefix=/home/travis/samtools && make && make install && cd ..
# We don't really need the modules below this, just one module needs it (modules/Bio/EnsEMBL/Analysis/Tools/BlastDBTracking.pm) and it is not used by us
    - echo "We need these modules for an unused module"
    - cpanm --quiet --notest MooseX::ClassAttribute
    - cpanm --quiet --notest File::Spec::Link
    - cpanm --quiet --notest Readonly
# Environment variables needed for 'install'
    - export HTSLIB_DIR=$PWD/htslib-1.3.2
    - export PERL5LIB=$PWD/bioperl-live

before_script:
# Needed for test needing connection to a DB
    - cp travisci/MultiTestDB.conf.mysql modules/t/MultiTestDB.conf.mysql
    - mkdir -p modules/t/test-genome-DBs/homo_sapiens
    - cp -r ensembl/modules/t/test-genome-DBs/homo_sapiens/core modules/t/test-genome-DBs/homo_sapiens
    - unset HTSLIB_DIR
    - unset PERL5LIB
    - export PATH=$HOME/samtools/bin:$PATH

script: "./travisci/harness.sh"

notifications:
  email:
    on_success: always
    on_failure: always